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 20:41 -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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbHmdb_1.10.2.tar.gz |
| StartedAt: 2024-10-17 14:03:23 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 14:04:48 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 85.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbHmdb.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbHmdb_1.10.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbHmdb.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 [14:04:16.243] Loading definitions from package biodb version 1.12.0.
INFO [14:04:16.444] Loading definitions from package biodbChebi version 1.10.0.
INFO [14:04:16.459] Loading definitions from package biodbExpasy version 1.8.1.
INFO [14:04:16.468] Loading definitions from package biodbHmdb version 1.10.2.
INFO [14:04:16.480] Loading definitions from package biodbKegg version 1.10.2.
INFO [14:04:16.539] Loading definitions from package biodbLipidmaps version 1.10.0.
INFO [14:04:16.550] Loading definitions from package biodbNcbi version 1.8.0.
INFO [14:04:16.578] Loading definitions from package biodbNci version 1.8.0.
INFO [14:04:16.587] Loading definitions from package biodbUniprot version 1.10.0.
Loading required package: biodb
Error in hmdb$getEntry(id)$cloneInstance(hmdbSqlite$getDbClass()) :
attempt to apply non-function
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_300_search.R:42:1'): We can search for multiple words inside description field. ──
Error in `FUN(X[[i]], ...)`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodbHmdb (local) `<fn>`(conn = `<HmdbMtbC>`)
3. └─conn$searchForEntries(fields = list(description = words), max.results = 3) at test_300_search.R:4:5
4. └─private$doSearchForEntries(fields = fields, max.results = max.results)
5. └─base::vapply(names(fields), tryMatch, FUN.VALUE = TRUE)
6. └─biodbHmdb (local) FUN(X[[i]], ...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 73 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbHmdb.Rcheck/00check.log’
for details.
biodbHmdb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbHmdb ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘biodbHmdb’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c EntryMaker.cpp -o EntryMaker.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FileEntryMaker.cpp -o FileEntryMaker.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c TagDetector.cpp -o TagDetector.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XmlSplitter.cpp -o XmlSplitter.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extractXmlEntries.cpp -o extractXmlEntries.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-100-TagDetector.cpp -o test-100-TagDetector.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-runner.cpp -o test-runner.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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 [2024-10-17 14:04:28.609][biodb::testContext]
biodb.INFO [2024-10-17 14:04:28.613][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:28.614][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2024-10-17 14:04:28.614][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:28.614][biodb::testContext]
biodb.INFO [2024-10-17 14:04:28.617][biodb::testThat]
biodb.INFO [2024-10-17 14:04:28.618][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2024-10-17 14:04:28.618][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:28.620][biodb::testThat]
biodb.INFO [2024-10-17 14:04:28.706][biodb::testContext]
biodb.INFO [2024-10-17 14:04:28.707][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:28.708][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-10-17 14:04:28.709][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:28.710][biodb::testContext]
biodb.INFO [2024-10-17 14:04:28.721][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:28.721][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:28.729][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:28.730][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 14:04:28.730][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 14:04:28.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.733][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[2024-10-17 14:04:28.734][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 14:04:28.759][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 14:04:28.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.764][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 14:04:28.764][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 14:04:28.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.767][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 14:04:28.768][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 14:04:28.769][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 14:04:28.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.772][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 14:04:28.773][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 14:04:28.774][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 14:04:28.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.776][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[2024-10-17 14:04:28.777][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 14:04:28.778][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 14:04:28.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.781][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 14:04:28.782][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 14:04:28.783][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 14:04:28.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.786][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 14:04:28.786][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 14:04:28.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.789][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 14:04:28.790][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 14:04:28.791][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 14:04:28.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.794][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:28.795][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 14:04:28.795][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 14:04:28.796][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 14:04:28.797][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 14:04:28.798][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 14:04:28.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.800][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 14:04:28.801][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 14:04:28.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.817][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 14:04:28.818][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 14:04:28.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.820][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 14:04:28.821][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 14:04:28.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.826][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 14:04:28.827][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 14:04:28.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.830][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 14:04:28.831][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 14:04:28.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.834][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:28.835][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 14:04:28.851][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 14:04:28.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.852][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 14:04:28.853][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 14:04:28.854][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 14:04:28.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:28.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:28.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:28.860][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 14:04:28.893][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:28.906][self$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[2024-10-17 14:04:28.907][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:28.908][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:28.909][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:28.910][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:28.911][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:28.912][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:28.913][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:28.915][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:28.918][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:28.919][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 14:04:28.919][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:28.920][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:28.920][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:28.921][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:28.921][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:28.921][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:28.921][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:28.921][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:28.922][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:28.923][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:28.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:28.925][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:28.926][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:28.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:28.934][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:28.934][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:28.935][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:28.936][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:28.936][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:28.937][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:28.938][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 14:04:28.940][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:28.941][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:28.941][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:28.942][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:28.943][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:28.944][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:28.945][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:28.945][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:28.946][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:28.947][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:28.948][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:28.948][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 14:04:28.949][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:28.950][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:28.951][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:28.952][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:28.952][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:28.952][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:28.952][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:28.952][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:28.952][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:28.953][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:28.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:28.955][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:28.955][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:28.956][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:28.957][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:28.958][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:28.958][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:28.959][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:28.960][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:28.961][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:28.962][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 14:04:28.963][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:28.964][self$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[2024-10-17 14:04:28.965][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:28.966][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:28.967][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:28.967][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:28.968][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:28.969][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:28.970][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:28.970][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:28.971][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:28.972][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 14:04:28.973][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:28.975][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:28.978][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:28.988][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:28.990][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:28.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:28.991][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:28.992][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:28.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:28.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:28.995][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:28.995][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:28.996][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:28.997][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:28.998][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:28.999][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.000][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 14:04:29.002][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.002][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:29.003][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.003][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:29.003][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.004][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.004][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.004][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.005][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:29.005][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:29.005][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.006][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 14:04:29.008][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:29.009][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.009][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.010][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.010][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:29.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:29.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:29.011][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:29.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:29.013][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:29.015][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.016][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.017][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:29.017][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:29.018][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.019][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.022][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:29.023][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.106][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 14:04:29.116][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 14:04:29.118][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 14:04:29.119][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 14:04:29.131][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:04:29.133][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 14:04:29.134][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:29.135][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:29.137][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 14:04:29.138][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 14:04:29.139][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:04:29.140][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 14:04:29.143][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:29.144][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:29.147][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 14:04:29.149][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:04:29.150][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 14:04:29.151][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 14:04:29.152][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:04:29.153][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 14:04:29.154][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 14:04:29.156][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 14:04:29.157][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 14:04:29.158][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 14:04:29.159][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 14:04:29.160][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 14:04:29.161][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 14:04:29.162][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 14:04:29.164][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 14:04:29.165][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 14:04:29.166][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 14:04:29.167][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 14:04:29.168][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 14:04:29.169][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 14:04:29.170][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 14:04:29.170][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 14:04:29.171][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 14:04:29.171][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 14:04:29.172][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 14:04:29.172][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 14:04:29.173][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 14:04:29.173][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 14:04:29.174][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 14:04:29.174][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 14:04:29.176][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 14:04:29.177][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 14:04:29.179][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 14:04:29.180][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 14:04:29.181][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 14:04:29.181][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 14:04:29.182][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 14:04:29.183][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 14:04:29.183][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 14:04:29.184][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 14:04:29.184][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 14:04:29.185][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 14:04:29.185][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 14:04:29.186][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 14:04:29.188][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 14:04:29.189][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 14:04:29.190][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 14:04:29.191][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 14:04:29.205][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 14:04:29.206][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 14:04:29.207][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 14:04:29.209][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 14:04:29.210][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:04:29.211][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:04:29.212][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 14:04:29.212][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 14:04:29.213][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 14:04:29.213][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 14:04:29.214][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 14:04:29.214][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 14:04:29.215][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 14:04:29.215][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 14:04:29.215][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 14:04:29.216][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 14:04:29.218][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 14:04:29.219][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 14:04:29.220][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 14:04:29.221][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 14:04:29.222][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 14:04:29.226][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 14:04:29.227][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:29.232][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:29.233][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.233][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.243][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[2024-10-17 14:04:29.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.342][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:29.353][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 14:04:29.355][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.356][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.357][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.358][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:29.358][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.359][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-10-17 14:04:29.360][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.361][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.362][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 14:04:29.363][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:29.363][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.364][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-10-17 14:04:29.365][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-10-17 14:04:29.366][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-10-17 14:04:29.367][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.368][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:29.368][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-10-17 14:04:29.368][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-10-17 14:04:29.369][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 14:04:29.369][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:29.370][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:29.371][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:29.372][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:29.372][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:29.373][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.374][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-17 14:04:29.374][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-10-17 14:04:29.375][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:29.375][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:29.376][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.377][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.383][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-10-17 14:04:29.384][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 14:04:29.386][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 14:04:29.387][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:04:29.388][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:04:29.410][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 14:04:29.411][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-10-17 14:04:29.417][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 14:04:29.422][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 14:04:29.428][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:29.429][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:29.431][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-10-17 14:04:29.432][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-10-17 14:04:29.432][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-17 14:04:29.432][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-10-17 14:04:29.433][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:29.433][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:29.434][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-10-17 14:04:29.434][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-10-17 14:04:29.435][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 14:04:29.464][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 14:04:29.470][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:29.471][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:29.471][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 14:04:29.472][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:29.472][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-10-17 14:04:29.473][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 14:04:29.474][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-10-17 14:04:29.480][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-10-17 14:04:29.481][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 14:04:29.482][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:29.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:29.484][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.485][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 14:04:29.491][biodb::testContext]
biodb.INFO [2024-10-17 14:04:29.491][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:29.492][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2024-10-17 14:04:29.492][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:29.493][biodb::testContext]
biodb.INFO [2024-10-17 14:04:29.498][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:29.499][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:29.503][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:29.504][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 14:04:29.504][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 14:04:29.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.505][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[2024-10-17 14:04:29.506][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 14:04:29.506][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 14:04:29.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.512][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 14:04:29.513][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 14:04:29.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.517][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 14:04:29.517][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 14:04:29.518][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 14:04:29.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.521][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 14:04:29.522][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 14:04:29.523][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 14:04:29.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.526][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 14:04:29.527][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 14:04:29.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.548][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 14:04:29.550][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 14:04:29.551][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 14:04:29.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.553][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 14:04:29.553][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 14:04:29.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.557][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 14:04:29.557][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 14:04:29.558][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 14:04:29.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.559][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:29.560][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 14:04:29.561][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 14:04:29.561][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 14:04:29.562][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 14:04:29.562][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 14:04:29.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.564][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 14:04:29.564][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 14:04:29.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.566][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 14:04:29.566][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 14:04:29.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.569][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 14:04:29.569][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 14:04:29.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.570][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 14:04:29.571][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 14:04:29.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.574][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 14:04:29.575][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 14:04:29.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.576][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:29.576][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 14:04:29.598][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 14:04:29.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.600][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 14:04:29.600][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 14:04:29.601][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 14:04:29.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.605][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 14:04:29.607][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.608][self$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[2024-10-17 14:04:29.610][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.612][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:29.613][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.615][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.616][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.618][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.619][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:29.620][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:29.620][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.622][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 14:04:29.624][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:29.638][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.639][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.640][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:29.640][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:29.640][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:29.640][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:29.640][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:29.643][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:29.644][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:29.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:29.655][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:29.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:29.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:29.658][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.659][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.661][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:29.661][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:29.662][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.662][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.663][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 14:04:29.665][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.665][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:29.666][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.666][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:29.666][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.667][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.667][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.667][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.668][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:29.669][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:29.670][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.671][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 14:04:29.672][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:29.672][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.673][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.673][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:29.673][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:29.673][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:29.673][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:29.673][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:29.674][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:29.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:29.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:29.675][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:29.675][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:29.676][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:29.678][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.679][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.680][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:29.681][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:29.682][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.683][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.684][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 14:04:29.686][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.686][self$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[2024-10-17 14:04:29.687][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.688][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:29.689][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.690][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.691][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.692][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.692][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:29.693][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:29.694][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.695][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 14:04:29.696][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:29.697][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.699][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.701][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.702][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:29.703][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:29.704][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:29.705][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:29.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:29.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:29.708][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.709][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.710][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:29.710][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:29.711][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.712][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.713][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 14:04:29.715][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.716][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:29.717][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.735][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:29.739][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.742][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.744][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.747][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.748][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:29.749][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:29.751][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.752][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 14:04:29.754][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:29.755][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.755][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:29.756][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.757][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:29.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:29.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:29.762][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:29.764][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:29.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:29.766][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:29.767][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.768][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:29.769][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:29.770][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:29.770][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:29.772][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:29.772][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.781][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[2024-10-17 14:04:29.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.795][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[2024-10-17 14:04:29.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:29.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:29.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:29.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:29.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:29.854][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 14:04:29.855][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 14:04:29.855][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 14:04:29.856][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 14:04:29.856][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:04:29.857][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 14:04:29.858][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:29.859][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:29.860][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 14:04:29.861][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 14:04:29.862][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:04:29.863][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 14:04:29.863][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:29.864][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:29.865][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 14:04:29.868][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:04:29.870][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 14:04:29.871][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 14:04:29.871][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:04:29.872][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 14:04:29.873][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 14:04:29.873][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 14:04:29.874][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 14:04:29.875][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 14:04:29.876][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 14:04:29.876][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 14:04:29.877][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 14:04:29.878][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 14:04:29.878][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 14:04:29.879][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 14:04:29.880][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 14:04:29.883][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 14:04:29.885][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 14:04:29.887][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 14:04:29.888][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 14:04:29.889][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 14:04:29.891][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 14:04:29.892][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 14:04:29.893][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 14:04:29.894][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 14:04:29.910][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 14:04:29.914][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 14:04:29.916][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 14:04:29.917][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 14:04:29.918][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 14:04:29.922][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 14:04:29.923][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 14:04:29.925][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 14:04:29.926][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 14:04:29.927][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 14:04:29.929][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 14:04:29.930][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 14:04:29.930][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 14:04:29.931][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 14:04:29.935][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 14:04:29.936][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 14:04:29.937][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 14:04:29.937][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 14:04:29.938][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 14:04:29.940][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 14:04:29.942][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 14:04:29.943][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 14:04:29.944][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 14:04:29.945][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 14:04:29.947][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 14:04:29.948][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 14:04:29.949][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:04:29.950][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:04:29.952][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 14:04:29.953][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 14:04:29.954][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 14:04:29.955][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 14:04:29.957][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 14:04:29.958][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 14:04:29.959][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 14:04:29.961][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 14:04:29.962][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 14:04:29.963][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 14:04:29.966][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 14:04:29.970][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 14:04:29.973][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 14:04:29.975][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 14:04:29.976][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 14:04:29.977][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 14:04:29.996][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:29.999][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:30.001][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.002][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:30.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:30.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:30.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:30.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:30.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:30.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:30.130][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:30.132][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 14:04:30.134][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:30.135][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 14:04:30.135][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:30.136][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:30.137][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:30.138][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-10-17 14:04:30.139][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:30.140][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:30.140][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 14:04:30.141][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:30.142][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:30.145][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-10-17 14:04:30.146][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-10-17 14:04:30.148][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-10-17 14:04:30.150][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:30.151][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:30.151][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-10-17 14:04:30.151][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-10-17 14:04:30.152][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 14:04:30.154][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:30.155][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:30.156][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:30.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:30.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:30.158][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:30.177][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-17 14:04:30.177][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-10-17 14:04:30.179][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:30.180][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:30.181][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:30.182][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:30.183][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-10-17 14:04:30.185][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 14:04:30.186][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 14:04:30.187][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:04:30.189][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:04:30.192][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 14:04:30.193][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-10-17 14:04:30.194][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 14:04:30.195][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 14:04:30.196][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:30.197][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:30.198][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-10-17 14:04:30.199][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-10-17 14:04:30.201][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-17 14:04:30.201][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-10-17 14:04:30.203][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:30.203][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:30.204][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-10-17 14:04:30.213][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-10-17 14:04:30.214][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 14:04:30.215][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 14:04:30.216][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:30.218][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:30.221][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 14:04:30.223][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:30.224][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-10-17 14:04:30.225][biodb::testThat]
biodb.INFO [2024-10-17 14:04:30.226][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2024-10-17 14:04:30.227][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:30.229][biodb::testThat]
biodb.DEBUG[2024-10-17 14:04:30.246][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 14:04:30.247][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 14:04:30.248][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-10-17 14:04:30.250][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 14:04:30.251][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-10-17 14:04:30.255][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-10-17 14:04:32.018][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-10-17 14:04:32.021][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml, HMDB0000005.xml, HMDB0000008.xml, HMDB0000010.xml, HMDB0000011.xml
biodb.DEBUG[2024-10-17 14:04:32.456][private$doGetEntryIds] COUNT IDS = 179631
biodb.DEBUG[2024-10-17 14:04:32.505][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-10-17 14:04:32.526][biodb::testThat]
biodb.INFO [2024-10-17 14:04:32.527][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2024-10-17 14:04:32.528][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:32.529][biodb::testThat]
biodb.DEBUG[2024-10-17 14:04:32.546][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2024-10-17 14:04:32.548][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-10-17 14:04:32.549][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 14:04:32.550][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-10-17 14:04:32.553][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2024-10-17 14:04:32.556][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:32.558][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-10-17 14:04:32.559][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:04:32.561][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:04:32.564][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-10-17 14:04:32.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:32.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:32.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:32.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:32.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:32.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:32.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:32.643][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:32.659][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:32.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.662][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:32.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:32.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.680][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:32.681][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:32.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.683][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.711][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:32.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:32.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.718][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:32.719][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:32.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.720][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.721][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:32.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:32.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.726][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:32.727][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:32.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.728][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.730][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:32.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:32.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.733][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:32.733][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:32.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.735][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:32.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:32.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.739][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:32.740][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:32.741][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.742][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:32.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:32.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.771][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:32.772][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:32.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.773][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.775][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:32.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:32.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.778][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:32.779][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:32.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.781][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.782][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:32.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:32.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.789][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:32.790][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:32.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.793][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.795][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:32.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:32.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.800][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:32.801][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:32.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.802][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.803][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:32.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:32.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.823][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:32.825][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:32.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.828][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.830][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:32.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:32.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.833][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:32.834][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:32.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.836][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.837][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:32.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:32.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.841][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:32.842][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:32.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.843][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.844][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:32.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:32.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.872][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:32.873][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:32.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.875][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:32.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:32.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.885][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:32.886][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:32.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.888][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:32.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:32.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.893][ef$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:32.894][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:32.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.895][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.897][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:32.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:32.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.900][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:32.901][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:32.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.903][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.904][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:32.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:32.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.911][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-10-17 14:04:32.913][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:32.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.914][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.916][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-10-17 14:04:32.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:32.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:32.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:32.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:32.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:32.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:32.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:32.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.969][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:32.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:32.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:32.980][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:32.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:32.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:32.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.003][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:33.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:33.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.007][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:33.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:33.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.011][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:33.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:33.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.014][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:33.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:33.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:33.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:33.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:33.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:33.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:33.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:33.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:33.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:33.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:33.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:33.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:33.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:33.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.043][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:33.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:33.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.047][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:33.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:33.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.050][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:33.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:33.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.054][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:33.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:33.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.057][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:33.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:33.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.078][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:33.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:33.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.082][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:33.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:33.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.086][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:33.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:33.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.092][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:33.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:33.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.095][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:33.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:33.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.099][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:33.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:33.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.103][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:33.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:33.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.105][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:33.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:33.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.107][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:33.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:33.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.111][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:33.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:33.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.115][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:33.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:33.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:33.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:33.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:33.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:33.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.134][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.141][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:33.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:33.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.147][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:33.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:33.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.172][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:33.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:33.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:33.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:33.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:33.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:33.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:33.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:33.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.186][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:33.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:33.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:33.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:33.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:33.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:33.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.197][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:33.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:33.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.205][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:33.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:33.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.208][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:33.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:33.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.212][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:33.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:33.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.215][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:33.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:33.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.218][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:33.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:33.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.222][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:33.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:33.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.225][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:33.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:33.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.228][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:33.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:33.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.234][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-17 14:04:33.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.239][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.275][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-17 14:04:33.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:33.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:33.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:33.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.301][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:33.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:33.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:33.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:33.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.305][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:33.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:33.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.310][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:33.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:33.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.317][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:33.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:33.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.340][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:33.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:33.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:33.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:33.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.368][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:33.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:33.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:33.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:33.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:33.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:33.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:33.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:33.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:33.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:33.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:33.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:33.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:33.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:33.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:33.393][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2024-10-17 14:04:33.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:33.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:33.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:33.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:33.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:33.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:33.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:33.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:33.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 14:04:33.417][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 14:04:33.418][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-10-17 14:04:33.419][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-10-17 14:04:33.421][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 14:04:33.422][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:33.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:33.423][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.425][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 14:04:33.431][biodb::testContext]
biodb.INFO [2024-10-17 14:04:33.447][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:33.449][biodb::testContext] Test context - Test search of entries
biodb.INFO [2024-10-17 14:04:33.450][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:33.450][biodb::testContext]
biodb.INFO [2024-10-17 14:04:33.457][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:33.459][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:33.465][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:33.466][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 14:04:33.467][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 14:04:33.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.470][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 14:04:33.471][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 14:04:33.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.475][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 14:04:33.475][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 14:04:33.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.479][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 14:04:33.479][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 14:04:33.480][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 14:04:33.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.483][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 14:04:33.484][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 14:04:33.485][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 14:04:33.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.489][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 14:04:33.490][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 14:04:33.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.493][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 14:04:33.494][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 14:04:33.495][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 14:04:33.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.498][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 14:04:33.499][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 14:04:33.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.502][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 14:04:33.503][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 14:04:33.504][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 14:04:33.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.508][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:33.509][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 14:04:33.510][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 14:04:33.511][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 14:04:33.526][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 14:04:33.527][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 14:04:33.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.549][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 14:04:33.551][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 14:04:33.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.555][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 14:04:33.556][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 14:04:33.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.558][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 14:04:33.559][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 14:04:33.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.560][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 14:04:33.561][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 14:04:33.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.563][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 14:04:33.563][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 14:04:33.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.567][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:33.569][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 14:04:33.587][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 14:04:33.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.593][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 14:04:33.594][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 14:04:33.595][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 14:04:33.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.598][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 14:04:33.600][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:33.601][self$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[2024-10-17 14:04:33.601][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.602][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:33.603][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.604][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:33.605][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:33.606][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:33.607][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:33.607][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:33.608][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.609][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 14:04:33.610][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:33.611][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.612][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.612][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:33.612][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:33.612][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:33.612][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:33.612][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:33.613][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:33.614][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:33.616][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:33.631][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:33.634][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:33.637][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:33.638][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:33.638][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.640][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:33.641][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:33.642][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:33.642][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.643][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 14:04:33.644][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:33.644][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:33.645][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.645][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:33.645][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.646][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:33.647][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:33.649][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:33.649][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:33.650][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:33.651][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.652][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 14:04:33.653][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:33.654][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.655][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.655][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:33.655][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:33.655][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:33.655][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:33.655][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:33.656][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:33.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:33.656][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:33.657][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:33.657][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:33.658][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:33.658][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:33.658][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.659][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:33.659][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:33.660][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:33.660][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.660][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 14:04:33.661][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.662][self$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[2024-10-17 14:04:33.662][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.663][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:33.663][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.664][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:33.664][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:33.664][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:33.665][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:33.665][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:33.666][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:33.666][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 14:04:33.667][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:33.667][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.667][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.668][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.669][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:33.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:33.672][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:33.673][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:33.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:33.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:33.675][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:33.677][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.679][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:33.681][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:33.681][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:33.699][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.700][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 14:04:33.702][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.702][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:33.703][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.703][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:33.705][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.706][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:33.719][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:33.721][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:33.722][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:33.724][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:33.726][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:33.727][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 14:04:33.728][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:33.729][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.730][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:33.731][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.732][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:33.733][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:33.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:33.734][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:33.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:33.736][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:33.737][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:33.738][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.738][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:33.739][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:33.740][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:33.741][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:33.742][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:33.743][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.743][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[2024-10-17 14:04:33.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.747][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[2024-10-17 14:04:33.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.751][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[2024-10-17 14:04:33.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.762][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[2024-10-17 14:04:33.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.767][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[2024-10-17 14:04:33.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.776][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[2024-10-17 14:04:33.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.820][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 14:04:33.821][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 14:04:33.822][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 14:04:33.822][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 14:04:33.823][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:04:33.824][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 14:04:33.825][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:33.827][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:33.829][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 14:04:33.830][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 14:04:33.831][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:04:33.832][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 14:04:33.847][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:33.848][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:33.849][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 14:04:33.849][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:04:33.850][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 14:04:33.853][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 14:04:33.855][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:04:33.856][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 14:04:33.858][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 14:04:33.859][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 14:04:33.861][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 14:04:33.862][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 14:04:33.863][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 14:04:33.864][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 14:04:33.866][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 14:04:33.867][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 14:04:33.868][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 14:04:33.869][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 14:04:33.871][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 14:04:33.872][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 14:04:33.873][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 14:04:33.875][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 14:04:33.876][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 14:04:33.877][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 14:04:33.878][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 14:04:33.880][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 14:04:33.881][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 14:04:33.882][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 14:04:33.883][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 14:04:33.883][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 14:04:33.884][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 14:04:33.885][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 14:04:33.886][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 14:04:33.887][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 14:04:33.887][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 14:04:33.888][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 14:04:33.889][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 14:04:33.890][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 14:04:33.891][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 14:04:33.892][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 14:04:33.893][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 14:04:33.894][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 14:04:33.896][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 14:04:33.897][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 14:04:33.898][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 14:04:33.899][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 14:04:33.900][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 14:04:33.902][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 14:04:33.903][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 14:04:33.904][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 14:04:33.925][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 14:04:33.927][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 14:04:33.928][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 14:04:33.929][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 14:04:33.931][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:04:33.932][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:04:33.933][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 14:04:33.935][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 14:04:33.936][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 14:04:33.937][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 14:04:33.939][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 14:04:33.940][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 14:04:33.941][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 14:04:33.943][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 14:04:33.944][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 14:04:33.945][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 14:04:33.947][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 14:04:33.948][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 14:04:33.949][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 14:04:33.951][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 14:04:33.952][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 14:04:33.953][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 14:04:33.957][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:33.958][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:33.959][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.960][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.960][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[2024-10-17 14:04:33.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:33.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:33.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:33.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:33.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:33.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:33.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:33.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:33.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:33.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:33.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:33.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:33.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:33.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:34.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:34.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:34.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:34.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:34.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:34.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:34.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:34.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:34.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:34.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:34.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:34.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:34.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:34.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:34.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:34.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:34.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:34.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:34.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:34.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:34.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:34.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:34.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:34.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:34.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:34.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:34.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:34.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:34.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:34.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:34.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:34.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:34.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:34.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:34.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:34.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:34.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:34.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:34.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:34.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:34.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:34.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:34.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:34.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:34.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:34.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:34.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:34.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:34.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:34.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:34.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:34.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:34.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:34.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:34.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:34.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:34.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:34.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:34.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:34.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:34.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:34.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:34.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:34.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:34.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:34.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:34.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:34.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:34.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:34.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:34.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:34.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:34.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:34.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:34.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:34.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:34.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:34.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:34.080][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:34.081][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 14:04:34.083][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:34.083][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 14:04:34.084][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:34.085][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:34.086][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:34.087][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-10-17 14:04:34.087][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:34.090][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:34.091][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 14:04:34.092][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:34.093][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:34.093][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-10-17 14:04:34.094][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-10-17 14:04:34.112][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-10-17 14:04:34.115][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:34.116][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:34.116][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-10-17 14:04:34.116][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-10-17 14:04:34.117][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 14:04:34.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:34.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:34.120][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:34.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:34.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:34.123][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:34.124][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-17 14:04:34.124][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-10-17 14:04:34.125][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:34.126][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:34.126][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:34.127][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:34.128][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-10-17 14:04:34.130][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 14:04:34.145][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 14:04:34.149][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:04:34.152][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:04:34.154][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 14:04:34.155][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-10-17 14:04:34.155][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 14:04:34.156][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 14:04:34.157][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:34.158][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:34.159][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-10-17 14:04:34.160][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-10-17 14:04:34.161][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-17 14:04:34.161][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-10-17 14:04:34.162][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:34.162][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:34.162][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-10-17 14:04:34.164][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-10-17 14:04:34.166][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 14:04:34.167][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 14:04:34.168][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:34.168][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:34.170][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 14:04:34.171][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:34.172][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-10-17 14:04:34.174][biodb::testThat]
biodb.INFO [2024-10-17 14:04:34.175][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2024-10-17 14:04:34.176][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:34.177][biodb::testThat]
biodb.DEBUG[2024-10-17 14:04:34.179][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-10-17 14:04:34.180][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2024-10-17 14:04:34.181][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2024-10-17 14:04:34.185][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 14:04:34.186][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 14:04:34.187][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-10-17 14:04:34.189][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 14:04:34.190][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-10-17 14:04:34.191][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-10-17 14:04:35.628][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-10-17 14:04:35.629][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml, HMDB0000005.xml, HMDB0000008.xml, HMDB0000010.xml, HMDB0000011.xml
biodb.DEBUG[2024-10-17 14:04:35.828][private$doGetEntryIds] COUNT IDS = 163400
biodb.DEBUG[2024-10-17 14:04:35.887][private$doSearchForEntries] All IDs = [163400]: "HMDB0000001, HMDB0000002, HMDB0000005, HMDB0000008, HMDB0000010, HMDB0000011, HMDB0000012, HMDB0000014, HMDB0000015, HMDB0000016, ..."
biodb.DEBUG[2024-10-17 14:04:35.888][private$doSearchForEntries] Total number of IDs = 163400
biodb.DEBUG[2024-10-17 14:04:35.890][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-10-17 14:04:35.892][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-10-17 14:04:35.895][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 14:04:35.897][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-10-17 14:04:35.901][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-10-17 14:04:35.902][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:35.906][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-10-17 14:04:35.907][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:04:35.908][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:04:35.910][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-10-17 14:04:35.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:35.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:35.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:35.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:35.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:35.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:36.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:36.006][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:36.026][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:36.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.030][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:36.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:36.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.045][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:36.048][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:36.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.051][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.053][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:36.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:36.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.059][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:36.060][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:36.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.062][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.064][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:36.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:36.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.068][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:36.069][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:36.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.072][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.074][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:36.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:36.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.080][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:36.081][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:36.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.083][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:36.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:36.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.088][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:36.089][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:36.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.091][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:36.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:36.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.095][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:36.096][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:36.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.098][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.099][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:36.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:36.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.103][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:36.103][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:36.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.105][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.106][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:36.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:36.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.110][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:36.111][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:36.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.113][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.116][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:36.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:36.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.122][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:36.123][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:36.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.124][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:36.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:36.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.130][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:36.132][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:36.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.135][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.252][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:36.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:36.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.260][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:36.261][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:36.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.265][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:36.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:36.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.275][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.278][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.281][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.284][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.291][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:36.293][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:36.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.297][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:36.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:36.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.305][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:36.307][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:36.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.312][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.314][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:36.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:36.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.322][ef$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:36.323][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:36.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.328][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.330][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:36.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:36.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.337][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:36.340][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:36.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.343][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.344][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:36.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:36.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.348][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-10-17 14:04:36.349][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:36.350][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.351][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.352][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-10-17 14:04:36.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:36.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:36.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:36.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:36.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:36.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:36.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:36.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.395][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:36.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:36.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.399][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:36.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:36.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.405][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:36.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:36.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.410][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:36.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:36.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.415][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:36.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:36.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.421][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:36.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:36.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:36.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:36.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:36.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:36.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:36.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:36.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:36.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:36.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:36.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:36.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:36.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:36.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.505][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:36.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:36.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.510][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:36.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:36.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.518][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:36.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:36.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.522][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:36.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:36.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.526][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:36.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:36.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.529][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:36.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:36.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.533][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:36.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:36.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.536][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:36.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:36.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.540][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:36.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:36.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.543][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:36.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:36.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.546][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:36.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:36.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.579][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:36.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:36.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.583][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:36.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:36.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.586][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:36.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:36.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.590][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:36.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:36.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:36.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:36.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:36.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:36.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:36.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:36.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.623][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.643][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.647][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:36.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:36.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.652][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:36.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:36.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.657][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:36.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:36.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:36.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:36.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:36.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:36.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:36.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:36.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:36.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:36.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:36.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:36.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:36.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:36.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.701][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:36.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:36.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.709][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:36.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:36.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.715][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:36.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:36.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.724][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:36.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:36.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.732][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:36.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:36.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.738][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:36.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:36.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.746][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:36.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:36.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.752][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:36.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:36.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.784][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:36.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:36.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.788][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-17 14:04:36.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.796][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.803][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.814][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-17 14:04:36.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:36.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:36.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:36.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:36.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:36.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.853][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:36.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:36.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.858][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:36.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:36.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:36.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:36.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.869][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:36.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:36.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.875][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:36.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:36.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:36.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:36.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.885][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:36.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:36.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:36.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:36.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:36.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:36.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:36.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:36.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:36.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:36.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:36.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:36.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:36.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:36.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:36.914][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-10-17 14:04:36.915][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:36.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:36.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.921][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:36.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:36.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.926][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:36.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:36.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:36.932][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:36.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:36.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:36.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:36.940][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-10-17 14:04:36.942][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-10-17 14:04:36.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:36.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:36.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:36.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:36.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:36.986][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:36.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:37.024][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2024-10-17 14:04:37.080][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-10-17 14:04:37.083][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 14:04:37.085][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-10-17 14:04:37.110][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2024-10-17 14:04:37.112][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:37.115][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-10-17 14:04:37.117][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:04:37.178][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:04:37.181][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-10-17 14:04:37.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:37.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:37.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:37.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:37.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:37.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:37.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:37.203][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.206][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.208][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.215][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:37.216][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:37.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.218][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.219][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:37.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:37.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.223][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:37.224][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:37.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.225][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.227][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:37.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:37.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.230][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:37.232][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:37.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.234][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.235][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:37.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:37.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.239][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:37.240][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:37.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.241][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:37.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:37.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.250][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:37.251][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:37.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.253][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:37.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:37.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.260][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:37.262][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:37.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.264][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.265][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:37.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:37.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.269][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:37.270][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:37.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.290][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.293][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:37.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:37.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.298][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:37.298][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:37.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.300][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.301][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:37.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:37.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.305][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:37.307][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:37.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.310][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:37.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:37.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.318][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:37.319][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:37.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.321][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.322][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:37.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:37.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.326][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:37.327][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:37.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.328][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:37.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:37.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.333][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.334][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.336][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.340][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:37.341][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:37.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.343][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:37.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:37.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.374][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:37.376][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:37.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.378][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:37.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:37.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.383][ef$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:37.385][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:37.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.388][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.390][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:37.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:37.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.396][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:37.397][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:37.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.398][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.400][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:37.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:37.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.403][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-10-17 14:04:37.404][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:37.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.406][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.407][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-10-17 14:04:37.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:37.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.444][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:37.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:37.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.451][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:37.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:37.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.456][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:37.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:37.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.461][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:37.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:37.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.468][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:37.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:37.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.474][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 14:04:37.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 14:04:37.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:37.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:37.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:37.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:37.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:37.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:37.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:37.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:37.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:37.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:37.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:37.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 14:04:37.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.525][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:37.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:37.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.528][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:37.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:37.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.533][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:37.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:37.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.536][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:37.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:37.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.538][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:37.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:37.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.541][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:37.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 14:04:37.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.544][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:37.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:37.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.552][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:37.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:37.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.554][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:37.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 14:04:37.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.558][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:37.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:37.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.562][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:37.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:37.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.565][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:37.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:37.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:37.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:37.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.591][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:37.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:37.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.596][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:37.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:37.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:37.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:37.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:37.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:37.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:37.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:37.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.643][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.661][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:37.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:37.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.664][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:37.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:37.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.667][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:37.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:37.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:37.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:37.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:37.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:37.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:37.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:37.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:37.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:37.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:37.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:37.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.683][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:37.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:37.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.686][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:37.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:37.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.691][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:37.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:37.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.693][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:37.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:37.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.696][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:37.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:37.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.702][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:37.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:37.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.705][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:37.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 14:04:37.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.709][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:37.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:37.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.711][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:37.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:37.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.756][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:37.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:37.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.763][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-17 14:04:37.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.767][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.771][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.780][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-17 14:04:37.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:37.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:37.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:37.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:37.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:37.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:37.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:37.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.798][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:37.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:37.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:37.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:37.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.807][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:37.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:37.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.811][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:37.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:37.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.817][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:37.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:37.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:37.870][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2024-10-17 14:04:37.896][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:37.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:37.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.901][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:37.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:37.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.905][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:37.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:37.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.908][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 14:04:37.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 14:04:37.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:37.912][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-10-17 14:04:37.913][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2024-10-17 14:04:37.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:37.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:37.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:37.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:37.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:37.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:37.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:37.929][private$loadEntries] Creating entries from ids [1]: "HMDB0000005".
biodb.DEBUG[2024-10-17 14:04:37.930][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-10-17 14:04:37.932][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 14:04:37.933][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-10-17 14:04:37.935][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000005".
biodb.TRACE[2024-10-17 14:04:37.936][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:04:37.938][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:04:37.938][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:04:37.939][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 14:04:37.940][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:04:37.958][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-10-17 14:04:37.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:37.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:37.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:37.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:37.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:37.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:37.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:37.973][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:37.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:37.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.976][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:37.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:37.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:37.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:37.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:37.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:37.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:37.993][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-10-17 14:04:37.994][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-10-17 14:04:38.026][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 14:04:38.028][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-10-17 14:04:38.029][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-10-17 14:04:38.030][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 14:04:38.030][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:38.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:38.032][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:38.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:38.035][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:38.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 73 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_300_search.R:42:1'): We can search for multiple words inside description field. ──
Error in `FUN(X[[i]], ...)`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodbHmdb (local) `<fn>`(conn = `<HmdbMtbC>`)
3. └─conn$searchForEntries(fields = list(description = words), max.results = 3) at test_300_search.R:4:5
4. └─private$doSearchForEntries(fields = fields, max.results = max.results)
5. └─base::vapply(names(fields), tryMatch, FUN.VALUE = TRUE)
6. └─biodbHmdb (local) FUN(X[[i]], ...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 73 ]
Error: Test failures
Execution halted
biodbHmdb.Rcheck/biodbHmdb-Ex.timings
| name | user | system | elapsed | |
| HmdbMetabolitesConn | 2.183 | 0.717 | 3.075 | |
| HmdbMetabolitesEntry | 0.382 | 0.025 | 0.437 | |