| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-06-06 11:00:27 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 193/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbHmdb 1.7.0 (landing page) Pierrick Roger
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: biodbHmdb |
| Version: 1.7.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings biodbHmdb_1.7.0.tar.gz |
| StartedAt: 2023-06-05 18:16:17 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 18:18:04 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 106.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbHmdb.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings biodbHmdb_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/biodbHmdb.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 8.1Mb
sub-directories of 1Mb or more:
libs 7.6Mb
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘biodbHmdb.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/biodbHmdb.Rcheck/00check.log’
for details.
biodbHmdb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL biodbHmdb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘biodbHmdb’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/testthat/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/testthat/include' -I/usr/local/include -fPIC -g -O2 -c Tag.cpp -o Tag.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/testthat/include' -I/usr/local/include -fPIC -g -O2 -c extractXmlEntries.cpp -o extractXmlEntries.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/testthat/include' -I/usr/local/include -fPIC -g -O2 -c test-100-tag.cpp -o test-100-tag.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/testthat/include' -I/usr/local/include -fPIC -g -O2 -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o biodbHmdb.so RcppExports.o Tag.o extractXmlEntries.o test-100-tag.o test-runner.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-biodbHmdb/00new/biodbHmdb/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbHmdb)
biodbHmdb.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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 [2023-06-05 18:17:40.627][biodb::testContext]
biodb.INFO [2023-06-05 18:17:40.630][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:17:40.631][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2023-06-05 18:17:40.632][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:17:40.633][biodb::testContext]
biodb.INFO [2023-06-05 18:17:40.636][biodb::testThat]
biodb.INFO [2023-06-05 18:17:40.637][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2023-06-05 18:17:40.638][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:40.639][biodb::testThat]
biodb.INFO [2023-06-05 18:17:40.767][biodb::testContext]
biodb.INFO [2023-06-05 18:17:40.769][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:17:40.770][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-06-05 18:17:40.771][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:17:40.773][biodb::testContext]
biodb.INFO [2023-06-05 18:17:40.792][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-06-05 18:17:40.795][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-06-05 18:17:40.803][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:17:40.804][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-06-05 18:17:40.806][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-06-05 18:17:40.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.811][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-06-05 18:17:40.836][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-06-05 18:17:40.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.841][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-06-05 18:17:40.843][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-06-05 18:17:40.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.847][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-06-05 18:17:40.849][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-06-05 18:17:40.850][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-06-05 18:17:40.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.854][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[2023-06-05 18:17:40.855][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-06-05 18:17:40.856][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-06-05 18:17:40.858][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-06-05 18:17:40.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.862][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-06-05 18:17:40.864][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-06-05 18:17:40.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.869][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-06-05 18:17:40.870][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-06-05 18:17:40.871][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-06-05 18:17:40.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.876][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-06-05 18:17:40.878][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-06-05 18:17:40.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.882][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-06-05 18:17:40.884][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-06-05 18:17:40.885][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-06-05 18:17:40.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.890][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-06-05 18:17:40.891][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-06-05 18:17:40.902][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-06-05 18:17:40.904][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-06-05 18:17:40.905][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-06-05 18:17:40.907][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-06-05 18:17:40.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.912][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-06-05 18:17:40.913][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-06-05 18:17:40.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.918][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-06-05 18:17:40.919][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-06-05 18:17:40.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.924][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-06-05 18:17:40.926][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-06-05 18:17:40.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.930][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-06-05 18:17:40.932][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-06-05 18:17:40.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.937][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-06-05 18:17:40.938][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-06-05 18:17:40.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.943][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-06-05 18:17:40.944][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-06-05 18:17:40.949][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-06-05 18:17:40.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.954][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-06-05 18:17:40.956][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-06-05 18:17:40.957][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-06-05 18:17:40.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:40.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:40.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:40.965][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-06-05 18:17:41.011][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.034][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-06-05 18:17:41.036][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.037][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:41.038][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.040][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.041][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.042][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.044][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:17:41.045][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:41.046][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.048][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-06-05 18:17:41.049][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:41.050][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.051][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.053][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:17:41.053][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:17:41.053][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-06-05 18:17:41.053][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-06-05 18:17:41.053][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-06-05 18:17:41.054][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:41.056][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:41.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:41.058][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:41.059][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:41.060][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:41.062][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.063][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.064][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:41.065][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:41.067][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.068][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.070][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-06-05 18:17:41.072][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.073][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-06-05 18:17:41.075][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.076][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:41.077][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.079][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.080][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.081][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.083][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-06-05 18:17:41.084][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:41.085][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.087][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-06-05 18:17:41.088][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:41.089][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.091][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.092][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:17:41.092][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:17:41.092][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-06-05 18:17:41.092][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-06-05 18:17:41.092][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-06-05 18:17:41.094][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:41.095][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:41.096][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:41.097][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:41.099][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:41.100][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:41.101][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.102][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.104][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:41.105][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:41.106][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.107][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.109][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-06-05 18:17:41.111][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.113][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-06-05 18:17:41.114][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.115][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:41.117][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.118][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.119][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.121][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.122][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:17:41.123][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:41.125][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.126][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-06-05 18:17:41.127][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:41.129][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.130][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.139][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.141][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:41.142][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:41.144][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:41.145][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:41.146][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:41.147][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:41.149][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.150][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.151][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:41.152][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:41.154][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.155][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.157][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-06-05 18:17:41.159][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.161][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-06-05 18:17:41.162][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.163][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:41.165][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.166][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.167][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.169][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.170][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-06-05 18:17:41.171][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:41.173][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.174][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-06-05 18:17:41.175][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:41.177][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.178][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.179][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.181][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:41.182][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:41.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:41.184][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:41.186][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:41.187][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:41.188][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.190][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.191][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:41.192][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:41.194][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.195][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.200][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:17:41.201][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.245][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[2023-06-05 18:17:41.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.286][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[2023-06-05 18:17:41.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.306][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-06-05 18:17:41.311][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-06-05 18:17:41.313][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-06-05 18:17:41.315][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-06-05 18:17:41.317][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-06-05 18:17:41.319][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-06-05 18:17:41.321][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-06-05 18:17:41.323][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-06-05 18:17:41.325][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-06-05 18:17:41.326][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-06-05 18:17:41.328][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-06-05 18:17:41.330][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-06-05 18:17:41.332][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-06-05 18:17:41.334][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-06-05 18:17:41.336][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-06-05 18:17:41.338][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-06-05 18:17:41.340][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-06-05 18:17:41.342][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-06-05 18:17:41.344][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-06-05 18:17:41.345][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-06-05 18:17:41.347][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-06-05 18:17:41.349][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-06-05 18:17:41.351][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-06-05 18:17:41.353][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-06-05 18:17:41.355][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-06-05 18:17:41.357][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-06-05 18:17:41.359][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-06-05 18:17:41.361][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-06-05 18:17:41.363][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-06-05 18:17:41.365][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-06-05 18:17:41.366][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-06-05 18:17:41.376][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-06-05 18:17:41.378][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-06-05 18:17:41.380][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-06-05 18:17:41.382][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-06-05 18:17:41.384][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-06-05 18:17:41.386][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-06-05 18:17:41.387][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-06-05 18:17:41.389][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-06-05 18:17:41.391][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-06-05 18:17:41.393][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-06-05 18:17:41.395][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-06-05 18:17:41.397][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-06-05 18:17:41.399][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-06-05 18:17:41.401][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-06-05 18:17:41.403][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-06-05 18:17:41.405][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-06-05 18:17:41.407][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-06-05 18:17:41.409][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-06-05 18:17:41.411][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-06-05 18:17:41.413][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-06-05 18:17:41.415][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-06-05 18:17:41.417][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-06-05 18:17:41.419][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-06-05 18:17:41.421][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-06-05 18:17:41.423][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-06-05 18:17:41.425][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-06-05 18:17:41.427][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-06-05 18:17:41.429][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-06-05 18:17:41.431][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-06-05 18:17:41.433][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-06-05 18:17:41.434][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-06-05 18:17:41.436][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-06-05 18:17:41.438][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-06-05 18:17:41.440][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-06-05 18:17:41.442][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-06-05 18:17:41.444][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-06-05 18:17:41.446][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-06-05 18:17:41.448][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-06-05 18:17:41.450][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-06-05 18:17:41.452][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-06-05 18:17:41.454][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-06-05 18:17:41.456][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-06-05 18:17:41.458][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-06-05 18:17:41.460][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-06-05 18:17:41.462][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-06-05 18:17:41.463][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-06-05 18:17:41.465][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-06-05 18:17:41.467][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-06-05 18:17:41.469][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-06-05 18:17:41.471][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-06-05 18:17:41.473][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-06-05 18:17:41.475][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-06-05 18:17:41.483][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-06-05 18:17:41.485][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-06-05 18:17:41.489][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:17:41.491][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.493][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.525][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[2023-06-05 18:17:41.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.560][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[2023-06-05 18:17:41.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:41.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:41.685][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-06-05 18:17:41.698][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-06-05 18:17:41.701][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.702][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.704][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.705][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:41.707][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.708][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-06-05 18:17:41.709][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.711][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.712][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-06-05 18:17:41.713][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:41.715][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.716][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-06-05 18:17:41.717][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-06-05 18:17:41.719][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-06-05 18:17:41.720][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:41.722][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:17:41.722][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-06-05 18:17:41.722][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2023-06-05 18:17:41.723][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-06-05 18:17:41.724][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:41.725][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:41.727][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:41.728][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:41.729][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:41.730][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:41.732][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-06-05 18:17:41.732][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-06-05 18:17:41.733][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:41.734][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:41.736][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:41.737][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:41.745][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2023-06-05 18:17:41.747][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-06-05 18:17:41.749][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-06-05 18:17:41.751][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-06-05 18:17:41.754][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-06-05 18:17:41.782][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-06-05 18:17:41.783][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-06-05 18:17:41.788][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-06-05 18:17:41.793][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-06-05 18:17:41.799][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:41.800][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:41.802][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-06-05 18:17:41.803][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-06-05 18:17:41.804][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-06-05 18:17:41.804][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-06-05 18:17:41.806][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:41.807][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:41.808][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-06-05 18:17:41.809][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-06-05 18:17:41.811][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-06-05 18:17:41.835][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-06-05 18:17:41.836][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:41.838][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:41.839][private$addConnectorRules] Create new rule for URL "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-06-05 18:17:41.841][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:41.842][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-06-05 18:17:41.862][biodb::testThat]
biodb.INFO [2023-06-05 18:17:41.863][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-06-05 18:17:41.864][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:41.866][biodb::testThat]
biodb.TRACE[2023-06-05 18:17:41.883][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2023-06-05 18:17:41.889][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-06-05 18:17:41.893][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-06-05 18:17:41.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:17:41.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:41.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:41.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:41.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:41.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:41.917][FUN] Functions in observer BiodbConfig: [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[2023-06-05 18:17:41.930][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:41.932][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:41.933][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:41.935][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:41.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:41.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:41.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:41.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:41.962][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:41.964][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:41.965][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:41.966][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.004][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.013][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:42.015][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:42.016][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.017][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.019][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:42.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:42.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.028][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:42.029][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:42.031][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.032][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.034][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:42.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:42.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.043][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:42.044][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:42.046][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.047][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:42.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:42.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.058][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.059][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.061][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.062][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.073][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:42.074][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:42.076][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.077][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.079][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:42.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:42.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.098][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:42.099][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:42.101][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.102][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.104][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:42.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:42.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.113][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:42.114][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:42.116][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.117][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.119][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:42.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:42.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.128][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:42.129][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:42.131][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.132][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.134][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:42.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:42.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.143][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:42.145][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:42.146][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.147][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.149][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:42.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:42.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.158][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:42.160][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:42.161][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.162][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:42.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:42.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.173][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.175][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.176][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.177][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.179][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.188][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:42.190][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:42.191][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.192][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:42.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:42.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.203][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:42.205][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:42.206][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.207][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.209][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:42.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:42.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.218][ef$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:42.220][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:42.221][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.222][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.224][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:42.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:42.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.233][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:42.234][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:42.236][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.237][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.239][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:42.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:42.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.248][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-06-05 18:17:42.250][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:42.251][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.252][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.254][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-06-05 18:17:42.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:42.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.334][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:42.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:42.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.339][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:42.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:42.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.345][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:42.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:42.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.350][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:42.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:42.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.355][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:42.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:42.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.361][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:42.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:42.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:42.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:42.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:42.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:42.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:42.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:42.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.398][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:42.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:42.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.403][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:42.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:42.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.409][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:42.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:42.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.414][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:42.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:42.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.419][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:42.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:42.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.424][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:42.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:42.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.430][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:42.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:42.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.435][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:42.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:42.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.440][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:42.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:42.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.445][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:42.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:42.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.450][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:42.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:42.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.456][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:42.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:42.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.461][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:42.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:42.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.466][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:42.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:42.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.478][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:42.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:42.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:42.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:42.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:42.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:42.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.495][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:42.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:42.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.500][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.517][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:42.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:42.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.522][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:42.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:42.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.527][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:42.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:42.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:42.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:42.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:42.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:42.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:42.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:42.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:42.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:42.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:42.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:42.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.560][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:42.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:42.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.565][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:42.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:42.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.571][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:42.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:42.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.576][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:42.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:42.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.581][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.587][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.592][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.598][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:42.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:42.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.603][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:42.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:42.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.608][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:42.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:42.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.614][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-06-05 18:17:42.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.619][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.625][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.635][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-06-05 18:17:42.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:42.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:42.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:42.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.682][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:42.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:42.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.687][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:42.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:42.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:42.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:42.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:42.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:42.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.707][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.712][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.723][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:42.765][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2023-06-05 18:17:42.772][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:17:42.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:17:42.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.777][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:17:42.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:17:42.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.783][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-06-05 18:17:42.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-06-05 18:17:42.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.788][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-06-05 18:17:42.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-06-05 18:17:42.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.824][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.879][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.885][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.890][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:42.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.923][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.925][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.926][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.927][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:42.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:42.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.944][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.950][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.956][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.962][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.963][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.964][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.966][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.967][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:42.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:42.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:42.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:42.999][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:43.001][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:43.002][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.003][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:43.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:43.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.020][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:43.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:43.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.025][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:43.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:43.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.031][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:43.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:43.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.036][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:43.038][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:43.039][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.040][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.042][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:43.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:43.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:43.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:43.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:43.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:43.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:43.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:43.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.081][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:43.083][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:43.084][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.085][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:43.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:43.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.102][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:43.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:43.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.108][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:43.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:43.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.113][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:43.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:43.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.119][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:43.120][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:43.122][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.123][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.124][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:43.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:43.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:43.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:43.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:43.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:43.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.150][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:43.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:43.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.156][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:43.157][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:43.159][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.160][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.161][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:43.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:43.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.177][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:43.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:43.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.183][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:43.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:43.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.188][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:43.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:43.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.194][ef$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:43.195][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:43.196][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.198][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.199][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:43.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:43.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.214][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:43.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:43.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.220][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:43.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:43.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.226][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:43.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:43.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.231][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:43.233][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:43.234][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.235][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.237][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:43.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:43.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.259][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:43.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:43.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.265][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:43.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:43.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.270][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:43.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:43.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.276][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:43.277][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:43.279][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.280][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.281][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:43.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:43.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:43.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:43.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:43.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:43.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:43.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:43.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.313][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:43.315][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:43.316][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.318][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:43.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:43.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.334][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:43.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:43.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.340][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:43.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:43.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.345][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:43.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:43.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.352][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:43.354][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:43.355][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.357][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.358][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:43.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:43.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.375][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:43.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:43.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.382][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:43.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:43.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.388][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:43.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:43.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.394][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:43.396][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:43.397][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.399][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.400][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:43.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:43.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.417][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:43.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:43.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.424][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:43.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:43.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.430][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:43.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:43.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.437][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:43.439][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:43.440][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.442][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.444][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:43.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:43.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.469][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:43.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:43.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.475][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:43.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:43.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.482][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:43.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:43.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.488][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:43.490][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:43.491][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.493][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.494][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:43.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:43.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:43.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:43.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:43.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:43.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.524][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:43.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:43.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.530][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:43.532][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:43.533][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.535][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:43.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:43.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.554][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:43.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:43.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.561][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:43.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:43.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:43.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:43.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.574][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:43.576][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:43.578][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.579][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.581][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:43.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:43.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.599][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:43.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:43.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.605][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:43.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:43.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.611][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:43.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:43.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.618][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:43.619][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:43.621][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.622][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.624][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:43.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:43.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.641][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:43.643][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:43.645][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.646][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.655][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:43.657][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:43.658][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.660][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.669][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:43.670][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:43.672][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.674][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.691][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:43.693][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:43.694][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.696][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.705][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:43.707][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:43.709][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.710][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.719][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:43.721][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:43.723][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.725][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.734][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:43.735][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:43.737][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.738][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.747][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:43.749][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:43.750][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.752][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.760][ef$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:43.762][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:43.764][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.765][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.774][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:43.776][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:43.777][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.778][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.787][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:43.789][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:43.790][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.792][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.801][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:43.802][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:43.804][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.805][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.814][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:43.816][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:43.817][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.819][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.827][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:43.829][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:43.830][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.832][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.840][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:43.842][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:43.844][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.845][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.854][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:43.855][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:43.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.858][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.867][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:43.869][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:43.870][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.872][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:43.880][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:43.882][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:43.883][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:43.885][ef$get] fields variable is a list.
biodb.INFO [2023-06-05 18:17:43.895][biodb::testThat]
biodb.INFO [2023-06-05 18:17:43.896][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-06-05 18:17:43.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:43.907][biodb::testThat]
biodb.DEBUG[2023-06-05 18:17:43.929][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-06-05 18:17:43.939][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2023-06-05 18:17:43.944][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2023-06-05 18:17:43.946][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2023-06-05 18:17:43.948][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2023-06-05 18:17:43.949][private$doDownload] Downloading HMDB metabolite database at "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2023-06-05 18:17:43.952][cch$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2023-06-05 18:17:43.954][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2023-06-05 18:17:43.957][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2023-06-05 18:17:43.960][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2023-06-05 18:17:43.961][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2023-06-05 18:17:43.964][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker157e1a21089231marker".
biodb.TRACE[2023-06-05 18:17:43.966][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2023-06-05 18:17:43.967][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-06-05 18:17:43.970][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2023-06-05 18:17:43.972][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2023-06-05 18:17:43.973][private$doExtractDownload] Extracting content of downloaded',
' HMDB metabolite database...
biodb.DEBUG[2023-06-05 18:17:43.976][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2023-06-05 18:17:43.977][private$doExtractDownload] Unzipping /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /home/biocbuild/.cache/R/biodb/tmp...
biodb.DEBUG[2023-06-05 18:17:43.981][private$findXmlDatabaseFile] Found files [1]: "hmdb_two_full_entries.xml" into /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2023-06-05 18:17:43.982][private$findXmlDatabaseFile] Found XML file /home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2023-06-05 18:17:43.984][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2023-06-05 18:17:43.986][private$doExtractDownload] Extract entries from XML file "/home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2023-06-05 18:17:43.995][self$addFilesToCache] Moving files to cache [2]: "/home/biocbuild/.cache/R/biodb/tmp/entry_1.xml, /home/biocbuild/.cache/R/biodb/tmp/entry_2.xml".
biodb.TRACE[2023-06-05 18:17:43.996][private$doAddFilesToCache] Destination files are [2]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-06-05 18:17:43.998][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-06-05 18:17:43.999][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2023-06-05 18:17:44.002][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker157e1afe860d8marker".
biodb.TRACE[2023-06-05 18:17:44.004][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2023-06-05 18:17:44.006][self$addFilesToCache] Done adding files.
biodb.TRACE[2023-06-05 18:17:44.008][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-06-05 18:17:44.010][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-06-05 18:17:44.013][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-06-05 18:17:44.015][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-06-05 18:17:44.080][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-06-05 18:17:44.082][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-06-05 18:17:44.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:17:44.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:44.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:44.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:44.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:44.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:44.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:17:44.105][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:44.107][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:44.109][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.110][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:44.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:44.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.133][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:44.135][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:44.136][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.138][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.140][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:44.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:44.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.150][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:44.152][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:44.154][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.155][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.157][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:44.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:44.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.168][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:44.170][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:44.171][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.173][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.175][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:44.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:44.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.186][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:44.187][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:44.189][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.190][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:44.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:44.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.203][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:44.205][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:44.207][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.208][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:44.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:44.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.221][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:44.223][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:44.224][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.226][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.228][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:44.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:44.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.238][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:44.240][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:44.242][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.243][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.246][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:44.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:44.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.261][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:44.264][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:44.265][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.267][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.269][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:44.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:44.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.280][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:44.282][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:44.284][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.285][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.287][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:44.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:44.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.297][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:44.299][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:44.301][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.302][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.304][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:44.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:44.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.314][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:44.316][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:44.317][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.319][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.321][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:44.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:44.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.332][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.333][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.335][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.336][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.363][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:44.365][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:44.366][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.367][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:44.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:44.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.380][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:44.381][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:44.383][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.384][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:44.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:44.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.396][ef$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:44.398][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:44.399][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.401][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.403][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:44.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:44.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.413][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:44.415][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:44.416][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.418][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.420][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:44.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:44.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.430][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-06-05 18:17:44.431][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:44.433][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.434][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.437][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-06-05 18:17:44.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:44.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:44.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:44.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:44.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:44.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:44.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:44.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.466][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:44.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:44.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.472][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:44.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:44.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.478][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:44.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:44.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.484][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:44.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:44.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.489][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:44.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:44.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.495][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:44.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:44.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:44.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:44.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:44.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:44.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:44.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:44.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:44.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:44.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:44.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:44.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:44.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:44.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.537][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:44.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:44.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.543][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:44.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:44.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.549][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:44.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:44.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.555][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:44.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:44.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.568][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:44.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:44.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.574][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:44.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:44.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.580][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:44.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:44.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.585][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:44.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:44.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.591][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:44.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:44.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.597][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:44.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:44.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.603][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:44.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:44.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.609][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:44.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:44.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.615][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:44.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:44.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.621][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:44.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:44.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.627][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:44.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:44.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:44.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:44.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.639][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:44.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:44.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.644][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:44.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:44.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.668][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:44.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:44.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.674][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:44.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:44.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.680][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:44.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:44.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:44.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:44.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:44.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:44.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:44.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:44.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.703][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:44.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:44.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:44.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:44.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:44.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:44.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.721][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:44.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:44.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.726][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:44.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:44.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.732][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:44.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:44.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.738][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:44.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:44.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.744][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:44.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:44.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.750][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:44.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:44.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.763][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:44.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:44.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.769][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:44.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:44.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.775][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:44.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:44.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.781][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-06-05 18:17:44.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.804][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-06-05 18:17:44.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:44.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.815][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:44.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:44.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:44.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:44.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.827][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:44.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:44.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.833][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:44.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:44.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:44.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:44.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.849][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:44.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:44.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.855][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:44.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:44.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:44.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:44.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.866][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:44.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:44.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:44.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:44.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:44.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:44.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:44.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:44.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:44.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:44.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:44.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:44.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:44.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:44.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:44.911][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-06-05 18:17:44.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-06-05 18:17:44.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-06-05 18:17:44.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-06-05 18:17:44.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-06-05 18:17:44.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:44.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-06-05 18:17:44.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-06-05 18:17:44.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-06-05 18:17:44.939][biodb::testThat]
biodb.INFO [2023-06-05 18:17:44.940][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-06-05 18:17:44.942][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:44.943][biodb::testThat]
biodb.TRACE[2023-06-05 18:17:44.947][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:44.949][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:44.950][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:44.959][ef$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:44.961][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2023-06-05 18:17:45.002][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:45.021][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2023-06-05 18:17:45.034][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-06-05 18:17:45.035][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-06-05 18:17:45.036][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-06-05 18:17:45.039][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:45.041][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:45.043][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-06-05 18:17:45.045][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:45.046][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-06-05 18:17:45.052][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-06-05 18:17:45.053][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-06-05 18:17:45.055][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-06-05 18:17:45.056][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-06-05 18:17:45.058][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-06-05 18:17:45.059][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-06-05 18:17:45.062][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:45.085][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-06-05 18:17:45.086][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-06-05 18:17:45.088][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2023-06-05 18:17:45.108][ef$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:45.110][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:45.111][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.113][ef$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:45.114][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2023-06-05 18:17:45.135][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:45.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:45.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.149][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:45.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:45.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.155][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:45.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:45.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:45.162][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.".
biodb.DEBUG[2023-06-05 18:17:45.249][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-06-05 18:17:45.251][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2023-06-05 18:17:45.252][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2023-06-05 18:17:45.272][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:45.275][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:45.277][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-06-05 18:17:45.278][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:45.280][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-06-05 18:17:45.313][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-06-05 18:17:45.315][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-06-05 18:17:45.316][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-06-05 18:17:45.318][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-06-05 18:17:45.319][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-06-05 18:17:45.320][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-06-05 18:17:45.323][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:45.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:45.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.328][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:45.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:45.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.334][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:45.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:45.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.339][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:45.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:45.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:45.344][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-06-05 18:17:45.346][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-06-05 18:17:45.347][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2023-06-05 18:17:45.368][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.370][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.371][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.372][ef$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:45.374][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2023-06-05 18:17:45.394][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.400][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.405][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:45.413][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2023-06-05 18:17:45.425][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2023-06-05 18:17:45.427][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2023-06-05 18:17:45.428][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2023-06-05 18:17:45.430][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:45.432][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:45.434][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-06-05 18:17:45.436][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:45.437][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-06-05 18:17:45.443][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-06-05 18:17:45.444][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-06-05 18:17:45.446][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-06-05 18:17:45.447][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-06-05 18:17:45.449][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-06-05 18:17:45.450][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-06-05 18:17:45.452][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.458][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.464][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.469][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:45.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:45.475][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-06-05 18:17:45.476][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-06-05 18:17:45.478][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2023-06-05 18:17:45.509][biodb::testThat]
biodb.INFO [2023-06-05 18:17:45.510][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-06-05 18:17:45.512][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:45.513][biodb::testThat]
biodb.TRACE[2023-06-05 18:17:45.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.552][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:45.588][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-06-05 18:17:45.590][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-06-05 18:17:45.592][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-06-05 18:17:45.595][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:45.597][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:45.600][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-06-05 18:17:45.602][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:45.604][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-06-05 18:17:45.610][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-06-05 18:17:45.612][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-06-05 18:17:45.613][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-06-05 18:17:45.615][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-06-05 18:17:45.617][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-06-05 18:17:45.618][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-06-05 18:17:45.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.634][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.641][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:45.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:45.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:45.647][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-06-05 18:17:45.649][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2023-06-05 18:17:45.674][biodb::testThat]
biodb.INFO [2023-06-05 18:17:45.675][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-06-05 18:17:45.677][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:45.678][biodb::testThat]
biodb.TRACE[2023-06-05 18:17:45.731][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:17:45.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:17:45.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.737][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:17:45.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:17:45.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.743][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-06-05 18:17:45.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-06-05 18:17:45.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.749][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-06-05 18:17:45.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-06-05 18:17:45.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.819][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:17:45.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:17:45.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.824][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:17:45.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:17:45.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.830][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-06-05 18:17:45.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-06-05 18:17:45.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:45.835][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-06-05 18:17:45.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-06-05 18:17:45.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:45.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-06-05 18:17:45.844][biodb::testThat]
biodb.INFO [2023-06-05 18:17:45.845][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-06-05 18:17:45.847][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:45.848][biodb::testThat]
biodb.INFO [2023-06-05 18:17:45.855][biodb::testThat]
biodb.INFO [2023-06-05 18:17:45.857][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-06-05 18:17:45.858][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:45.859][biodb::testThat]
biodb.INFO [2023-06-05 18:17:45.866][biodb::testThat]
biodb.INFO [2023-06-05 18:17:45.867][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-06-05 18:17:45.869][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:45.870][biodb::testThat]
biodb.DEBUG[2023-06-05 18:17:45.875][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2023-06-05 18:17:47.920][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2023-06-05 18:17:48.419][biodb::testThat]
biodb.INFO [2023-06-05 18:17:48.421][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-06-05 18:17:48.422][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:48.423][biodb::testThat]
biodb.DEBUG[2023-06-05 18:17:49.919][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2023-06-05 18:17:50.389][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:50.390][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:50.392][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.393][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.395][ef$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:50.396][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:50.399][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.401][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.402][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:50.404][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:50.405][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.407][ef$get] fields variable is a list.
biodb.INFO [2023-06-05 18:17:50.409][biodb::testThat]
biodb.INFO [2023-06-05 18:17:50.410][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-06-05 18:17:50.412][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:50.413][biodb::testThat]
biodb.DEBUG[2023-06-05 18:17:50.416][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-06-05 18:17:50.486][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-06-05 18:17:50.500][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:50.502][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-06-05 18:17:50.527][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-06-05 18:17:50.529][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-06-05 18:17:50.531][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-06-05 18:17:50.532][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-06-05 18:17:50.535][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:50.561][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-06-05 18:17:50.563][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-06-05 18:17:50.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:17:50.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:50.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:50.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:50.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:50.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:50.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:17:50.584][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:50.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:50.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.589][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:50.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:50.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:50.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:50.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:50.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:50.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:50.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:50.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:50.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:50.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:50.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:50.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:50.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:50.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:50.629][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-06-05 18:17:50.631][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-06-05 18:17:50.661][biodb::testThat]
biodb.INFO [2023-06-05 18:17:50.663][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-06-05 18:17:50.664][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:50.665][biodb::testThat]
biodb.DEBUG[2023-06-05 18:17:50.676][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2023-06-05 18:17:50.678][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2023-06-05 18:17:50.679][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-06-05 18:17:50.682][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:50.684][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-06-05 18:17:50.687][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2023-06-05 18:17:50.688][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-06-05 18:17:50.690][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-06-05 18:17:50.691][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-06-05 18:17:50.694][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:50.719][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-06-05 18:17:50.721][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-06-05 18:17:50.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:17:50.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:50.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:50.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:50.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:50.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:50.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:17:50.740][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:50.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:50.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.746][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:50.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:50.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:50.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:50.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:50.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:50.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:50.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:50.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:50.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:50.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:50.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:50.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:50.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:50.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:50.784][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-06-05 18:17:50.786][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-06-05 18:17:50.787][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2023-06-05 18:17:50.827][biodb::testThat]
biodb.INFO [2023-06-05 18:17:50.829][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-06-05 18:17:50.830][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:50.832][biodb::testThat]
biodb.INFO [2023-06-05 18:17:50.864][biodb::testThat]
biodb.INFO [2023-06-05 18:17:50.866][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-06-05 18:17:50.867][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:50.869][biodb::testThat]
biodb.DEBUG[2023-06-05 18:17:50.873][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:50.875][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:50.877][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-06-05 18:17:50.880][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:50.881][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-06-05 18:17:50.888][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-06-05 18:17:50.890][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-06-05 18:17:50.891][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-06-05 18:17:50.893][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2023-06-05 18:17:50.902][biodb::testThat]
biodb.INFO [2023-06-05 18:17:50.904][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-06-05 18:17:50.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:50.907][biodb::testThat]
biodb.DEBUG[2023-06-05 18:17:50.912][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:50.914][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:50.916][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-06-05 18:17:50.919][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:50.920][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-06-05 18:17:50.926][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-06-05 18:17:50.928][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-06-05 18:17:50.929][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-06-05 18:17:50.930][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2023-06-05 18:17:50.948][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:50.949][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:50.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.952][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.954][ef$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:50.955][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:50.957][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.958][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:50.960][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:50.961][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:50.962][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:50.964][ef$get] fields variable is a list.
biodb.INFO [2023-06-05 18:17:50.965][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-06-05 18:17:50.967][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-06-05 18:17:50.979][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-06-05 18:17:50.981][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-06-05 18:17:50.982][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:50.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:50.993][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:50.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:50.996][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:50.997][FUN] Functions in observer BiodbConfig: [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 [2023-06-05 18:17:51.002][biodb::testContext]
biodb.INFO [2023-06-05 18:17:51.003][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:17:51.005][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2023-06-05 18:17:51.006][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:17:51.007][biodb::testContext]
biodb.INFO [2023-06-05 18:17:51.016][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-06-05 18:17:51.018][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-06-05 18:17:51.023][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:17:51.025][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-06-05 18:17:51.026][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-06-05 18:17:51.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.031][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-06-05 18:17:51.033][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-06-05 18:17:51.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.037][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[2023-06-05 18:17:51.038][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-06-05 18:17:51.040][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-06-05 18:17:51.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.045][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-06-05 18:17:51.046][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-06-05 18:17:51.048][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-06-05 18:17:51.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.053][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-06-05 18:17:51.054][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-06-05 18:17:51.056][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-06-05 18:17:51.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.061][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-06-05 18:17:51.062][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-06-05 18:17:51.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.066][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[2023-06-05 18:17:51.067][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-06-05 18:17:51.069][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-06-05 18:17:51.070][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-06-05 18:17:51.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.075][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-06-05 18:17:51.077][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-06-05 18:17:51.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.082][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-06-05 18:17:51.084][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-06-05 18:17:51.085][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-06-05 18:17:51.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.090][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-06-05 18:17:51.092][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-06-05 18:17:51.093][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-06-05 18:17:51.094][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-06-05 18:17:51.096][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-06-05 18:17:51.097][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-06-05 18:17:51.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.103][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-06-05 18:17:51.104][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-06-05 18:17:51.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.109][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-06-05 18:17:51.111][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-06-05 18:17:51.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.116][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-06-05 18:17:51.117][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-06-05 18:17:51.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.123][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-06-05 18:17:51.124][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-06-05 18:17:51.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.128][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[2023-06-05 18:17:51.129][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-06-05 18:17:51.131][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-06-05 18:17:51.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.136][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-06-05 18:17:51.138][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-06-05 18:17:51.150][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-06-05 18:17:51.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.155][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-06-05 18:17:51.157][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-06-05 18:17:51.158][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-06-05 18:17:51.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.163][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-06-05 18:17:51.166][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.167][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-06-05 18:17:51.169][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.170][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:51.172][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.173][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.174][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.176][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.177][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:17:51.178][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:51.180][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.181][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-06-05 18:17:51.182][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:51.184][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.185][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.187][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:17:51.187][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:17:51.187][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-06-05 18:17:51.187][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-06-05 18:17:51.187][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-06-05 18:17:51.188][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:51.189][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:51.191][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:51.192][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:51.193][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:51.194][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:51.196][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.197][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.198][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:51.200][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:51.201][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.202][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.204][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-06-05 18:17:51.206][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.208][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-06-05 18:17:51.209][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.210][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:51.212][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.213][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.215][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.216][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.217][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-06-05 18:17:51.219][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:51.220][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.221][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-06-05 18:17:51.223][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:51.224][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.225][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.227][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:17:51.227][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:17:51.227][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-06-05 18:17:51.227][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-06-05 18:17:51.227][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-06-05 18:17:51.228][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:51.229][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:51.231][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:51.232][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:51.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:51.235][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:51.236][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.237][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.239][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:51.240][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:51.241][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.242][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.244][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-06-05 18:17:51.246][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.248][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-06-05 18:17:51.249][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.251][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:51.252][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.253][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.255][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.256][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.257][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:17:51.259][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:51.260][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.262][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-06-05 18:17:51.263][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:51.264][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.266][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.267][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.268][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:51.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:51.271][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:51.272][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:51.274][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:51.275][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:51.276][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.277][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.279][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:51.280][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:51.281][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.283][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.284][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-06-05 18:17:51.294][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.296][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-06-05 18:17:51.297][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.299][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:51.300][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.301][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.303][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.304][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.306][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-06-05 18:17:51.307][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:51.309][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.310][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-06-05 18:17:51.312][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:51.313][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.315][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.316][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.317][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:51.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:51.320][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:51.322][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:51.323][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:51.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:51.326][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.327][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.328][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:51.330][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:51.331][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.332][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.334][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:17:51.336][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.454][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-06-05 18:17:51.456][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-06-05 18:17:51.458][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-06-05 18:17:51.460][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-06-05 18:17:51.462][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-06-05 18:17:51.464][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-06-05 18:17:51.466][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-06-05 18:17:51.468][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-06-05 18:17:51.470][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-06-05 18:17:51.472][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-06-05 18:17:51.474][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-06-05 18:17:51.476][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-06-05 18:17:51.478][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-06-05 18:17:51.480][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-06-05 18:17:51.482][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-06-05 18:17:51.484][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-06-05 18:17:51.486][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-06-05 18:17:51.488][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-06-05 18:17:51.490][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-06-05 18:17:51.492][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-06-05 18:17:51.494][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-06-05 18:17:51.496][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-06-05 18:17:51.498][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-06-05 18:17:51.500][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-06-05 18:17:51.502][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-06-05 18:17:51.504][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-06-05 18:17:51.506][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-06-05 18:17:51.508][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-06-05 18:17:51.510][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-06-05 18:17:51.512][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-06-05 18:17:51.514][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-06-05 18:17:51.516][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-06-05 18:17:51.518][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-06-05 18:17:51.520][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-06-05 18:17:51.522][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-06-05 18:17:51.524][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-06-05 18:17:51.525][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-06-05 18:17:51.527][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-06-05 18:17:51.529][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-06-05 18:17:51.531][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-06-05 18:17:51.533][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-06-05 18:17:51.535][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-06-05 18:17:51.537][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-06-05 18:17:51.539][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-06-05 18:17:51.541][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-06-05 18:17:51.543][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-06-05 18:17:51.545][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-06-05 18:17:51.547][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-06-05 18:17:51.549][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-06-05 18:17:51.551][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-06-05 18:17:51.553][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-06-05 18:17:51.555][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-06-05 18:17:51.557][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-06-05 18:17:51.559][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-06-05 18:17:51.561][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-06-05 18:17:51.563][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-06-05 18:17:51.565][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-06-05 18:17:51.567][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-06-05 18:17:51.569][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-06-05 18:17:51.571][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-06-05 18:17:51.573][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-06-05 18:17:51.575][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-06-05 18:17:51.577][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-06-05 18:17:51.579][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-06-05 18:17:51.581][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-06-05 18:17:51.591][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-06-05 18:17:51.593][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-06-05 18:17:51.595][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-06-05 18:17:51.597][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-06-05 18:17:51.599][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-06-05 18:17:51.601][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-06-05 18:17:51.603][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-06-05 18:17:51.605][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-06-05 18:17:51.607][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-06-05 18:17:51.609][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-06-05 18:17:51.611][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-06-05 18:17:51.613][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-06-05 18:17:51.615][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-06-05 18:17:51.617][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-06-05 18:17:51.619][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-06-05 18:17:51.621][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-06-05 18:17:51.623][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-06-05 18:17:51.625][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-06-05 18:17:51.627][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-06-05 18:17:51.630][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-06-05 18:17:51.631][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:17:51.632][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.635][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:51.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.776][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[2023-06-05 18:17:51.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.785][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[2023-06-05 18:17:51.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:51.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.793][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[2023-06-05 18:17:51.795][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-06-05 18:17:51.797][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-06-05 18:17:51.800][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.801][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.803][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.804][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:51.806][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.807][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-06-05 18:17:51.808][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.810][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.811][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-06-05 18:17:51.812][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:51.814][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.815][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-06-05 18:17:51.816][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-06-05 18:17:51.818][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-06-05 18:17:51.819][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:51.821][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:17:51.821][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-06-05 18:17:51.821][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2023-06-05 18:17:51.822][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-06-05 18:17:51.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:51.825][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:51.826][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:51.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:51.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:51.830][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:51.831][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-06-05 18:17:51.831][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-06-05 18:17:51.833][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:51.834][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:51.835][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:51.837][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:51.838][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2023-06-05 18:17:51.840][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-06-05 18:17:51.843][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-06-05 18:17:51.845][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-06-05 18:17:51.847][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-06-05 18:17:51.851][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-06-05 18:17:51.853][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-06-05 18:17:51.854][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-06-05 18:17:51.856][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-06-05 18:17:51.858][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:51.859][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:51.861][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-06-05 18:17:51.863][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-06-05 18:17:51.864][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-06-05 18:17:51.864][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-06-05 18:17:51.865][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:51.867][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:51.868][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-06-05 18:17:51.869][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-06-05 18:17:51.871][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-06-05 18:17:51.880][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-06-05 18:17:51.882][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:51.884][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:51.886][private$addConnectorRules] Create new rule for URL "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-06-05 18:17:51.887][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:51.889][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-06-05 18:17:51.890][biodb::testThat]
biodb.INFO [2023-06-05 18:17:51.892][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2023-06-05 18:17:51.893][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:51.894][biodb::testThat]
biodb.DEBUG[2023-06-05 18:17:51.900][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:51.902][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:51.904][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-06-05 18:17:51.906][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:51.907][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-06-05 18:17:51.913][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-06-05 18:17:51.914][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-06-05 18:17:51.915][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-06-05 18:17:51.917][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-06-05 18:17:51.920][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2023-06-05 18:17:51.923][biodb::testThat]
biodb.INFO [2023-06-05 18:17:51.925][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2023-06-05 18:17:51.926][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:51.927][biodb::testThat]
biodb.DEBUG[2023-06-05 18:17:51.930][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-06-05 18:17:51.932][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-06-05 18:17:51.934][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:51.936][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-06-05 18:17:51.939][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-06-05 18:17:51.940][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-06-05 18:17:51.942][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-06-05 18:17:51.944][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-06-05 18:17:51.968][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-06-05 18:17:51.970][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-06-05 18:17:51.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:17:51.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:51.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:51.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:51.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:51.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:51.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:17:51.991][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:51.992][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:51.994][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:51.995][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:51.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:51.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:51.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.006][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:52.007][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:52.009][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.010][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.012][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:52.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:52.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.027][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:52.028][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:52.030][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.031][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.049][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:52.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:52.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.060][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:52.062][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:52.063][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.064][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.066][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:52.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:52.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.076][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:52.078][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:52.079][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.080][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:52.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:52.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.092][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:52.094][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:52.095][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.096][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:52.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:52.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.108][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:52.110][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:52.111][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.112][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.114][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:52.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:52.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.124][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:52.126][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:52.127][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.128][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.130][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:52.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:52.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.140][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:52.141][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:52.143][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.144][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.146][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:52.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:52.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.156][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:52.157][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:52.159][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.160][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.162][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:52.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:52.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.172][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:52.173][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:52.174][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.176][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.178][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:52.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:52.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.187][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:52.189][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:52.190][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.191][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:52.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:52.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.210][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.212][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.213][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.214][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.216][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.226][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:52.227][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:52.228][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.230][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:52.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:52.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.241][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:52.242][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:52.244][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.245][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.247][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:52.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:52.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.256][ef$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:52.257][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:52.259][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.260][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.262][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:52.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:52.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.271][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:52.272][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:52.274][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.275][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.277][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:52.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:52.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.286][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-06-05 18:17:52.288][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:52.289][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.290][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.292][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-06-05 18:17:52.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:52.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:52.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:52.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:52.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:52.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:52.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:52.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.318][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:52.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:52.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.324][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:52.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:52.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.329][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:52.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:52.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.335][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:52.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:52.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.340][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:52.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:52.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.346][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:52.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:52.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:52.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:52.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:52.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:52.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:52.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:52.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:52.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:52.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:52.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:52.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:52.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:52.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.393][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:52.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:52.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.398][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:52.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:52.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.404][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:52.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:52.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.409][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:52.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:52.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.415][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:52.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:52.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.420][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:52.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:52.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.426][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:52.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:52.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.431][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:52.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:52.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.437][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:52.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:52.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.442][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:52.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:52.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.448][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:52.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:52.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.453][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:52.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:52.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:52.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:52.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.465][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:52.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:52.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.470][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:52.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:52.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:52.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:52.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.481][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:52.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:52.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.487][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:52.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:52.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.492][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.517][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:52.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:52.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.523][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:52.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:52.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.528][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:52.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:52.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:52.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:52.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:52.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:52.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:52.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:52.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:52.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:52.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:52.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:52.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.562][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:52.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:52.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.568][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:52.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:52.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.573][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:52.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:52.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.579][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:52.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:52.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.585][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:52.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:52.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.590][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:52.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:52.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.596][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:52.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:52.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.602][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:52.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:52.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.607][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:52.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:52.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.613][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:52.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:52.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.618][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-06-05 18:17:52.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.624][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.635][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.648][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-06-05 18:17:52.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:52.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:52.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:52.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:52.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:52.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.670][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:52.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:52.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:52.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:52.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.682][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:52.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:52.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.691][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:52.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:52.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.697][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:52.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:52.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:52.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:52.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.709][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:52.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:52.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:52.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:52.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:52.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:52.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:52.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:52.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:52.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:52.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:52.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:52.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:52.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:52.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:52.752][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-06-05 18:17:52.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:52.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:52.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:52.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:52.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:52.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:52.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:52.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:52.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-06-05 18:17:52.774][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-06-05 18:17:52.775][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-06-05 18:17:52.777][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-06-05 18:17:52.778][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-06-05 18:17:52.779][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:52.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:52.782][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:52.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:52.784][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-06-05 18:17:52.798][biodb::testContext]
biodb.INFO [2023-06-05 18:17:52.800][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:17:52.801][biodb::testContext] Test context - Test search of entries
biodb.INFO [2023-06-05 18:17:52.803][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:17:52.804][biodb::testContext]
biodb.INFO [2023-06-05 18:17:52.812][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-06-05 18:17:52.815][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-06-05 18:17:52.819][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:17:52.821][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-06-05 18:17:52.822][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-06-05 18:17:52.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.826][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[2023-06-05 18:17:52.828][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-06-05 18:17:52.829][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-06-05 18:17:52.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.834][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-06-05 18:17:52.836][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-06-05 18:17:52.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.841][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-06-05 18:17:52.842][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-06-05 18:17:52.844][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-06-05 18:17:52.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.849][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-06-05 18:17:52.850][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-06-05 18:17:52.852][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-06-05 18:17:52.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.857][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-06-05 18:17:52.859][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-06-05 18:17:52.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.864][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-06-05 18:17:52.865][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-06-05 18:17:52.867][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-06-05 18:17:52.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.872][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-06-05 18:17:52.873][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-06-05 18:17:52.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.878][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-06-05 18:17:52.880][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-06-05 18:17:52.881][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-06-05 18:17:52.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.886][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-06-05 18:17:52.888][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-06-05 18:17:52.889][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-06-05 18:17:52.891][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-06-05 18:17:52.892][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-06-05 18:17:52.894][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-06-05 18:17:52.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.899][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-06-05 18:17:52.900][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-06-05 18:17:52.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.905][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-06-05 18:17:52.907][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-06-05 18:17:52.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.912][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-06-05 18:17:52.913][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-06-05 18:17:52.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.919][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-06-05 18:17:52.920][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-06-05 18:17:52.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.925][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-06-05 18:17:52.927][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-06-05 18:17:52.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.932][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-06-05 18:17:52.933][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-06-05 18:17:52.938][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-06-05 18:17:52.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.951][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-06-05 18:17:52.953][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-06-05 18:17:52.954][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-06-05 18:17:52.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:52.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:52.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:52.960][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-06-05 18:17:52.963][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:52.964][self$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[2023-06-05 18:17:52.965][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:52.967][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:52.968][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:52.970][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:52.971][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:52.973][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:52.974][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:17:52.976][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:52.977][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:52.979][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-06-05 18:17:52.980][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:52.981][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:52.983][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:52.984][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:17:52.984][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:17:52.984][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-06-05 18:17:52.984][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-06-05 18:17:52.984][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-06-05 18:17:52.986][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:52.987][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:52.989][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:52.990][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:52.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:52.993][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:52.994][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:52.995][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:52.997][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:52.998][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:52.999][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:53.001][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:53.003][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-06-05 18:17:53.005][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:53.007][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-06-05 18:17:53.008][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.010][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:53.012][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.013][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:53.015][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:53.016][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:53.018][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-06-05 18:17:53.019][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:53.020][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.022][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-06-05 18:17:53.023][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:53.025][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:53.026][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.028][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:17:53.028][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:17:53.028][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-06-05 18:17:53.028][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-06-05 18:17:53.028][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-06-05 18:17:53.029][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:53.031][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:53.032][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:53.033][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:53.035][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:53.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:53.038][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:53.039][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:53.040][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:53.042][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:53.043][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:53.045][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:53.046][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-06-05 18:17:53.049][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.050][self$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[2023-06-05 18:17:53.052][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.053][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:53.055][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.056][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:53.057][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:53.059][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:53.060][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:17:53.062][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:53.063][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:53.065][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-06-05 18:17:53.066][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:53.068][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:53.069][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.070][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:53.072][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:53.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:53.074][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:53.076][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:53.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:53.079][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:53.080][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:53.081][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:53.083][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:53.084][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:53.085][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:53.087][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:53.089][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-06-05 18:17:53.099][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.100][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-06-05 18:17:53.102][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.103][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:53.105][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.106][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:53.107][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:53.109][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:53.110][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-06-05 18:17:53.112][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:53.113][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:53.115][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-06-05 18:17:53.116][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:53.117][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:53.119][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.120][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:53.122][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:53.123][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:53.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:53.126][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:53.127][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:53.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:53.130][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:53.131][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:53.133][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:53.134][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:53.135][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:53.137][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:53.139][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:17:53.140][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.245][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[2023-06-05 18:17:53.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.259][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-06-05 18:17:53.261][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-06-05 18:17:53.264][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-06-05 18:17:53.266][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-06-05 18:17:53.268][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-06-05 18:17:53.270][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-06-05 18:17:53.272][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-06-05 18:17:53.274][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-06-05 18:17:53.276][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-06-05 18:17:53.278][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-06-05 18:17:53.280][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-06-05 18:17:53.282][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-06-05 18:17:53.284][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-06-05 18:17:53.286][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-06-05 18:17:53.288][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-06-05 18:17:53.290][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-06-05 18:17:53.292][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-06-05 18:17:53.294][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-06-05 18:17:53.296][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-06-05 18:17:53.298][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-06-05 18:17:53.300][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-06-05 18:17:53.302][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-06-05 18:17:53.304][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-06-05 18:17:53.306][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-06-05 18:17:53.308][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-06-05 18:17:53.310][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-06-05 18:17:53.312][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-06-05 18:17:53.314][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-06-05 18:17:53.316][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-06-05 18:17:53.318][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-06-05 18:17:53.320][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-06-05 18:17:53.322][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-06-05 18:17:53.324][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-06-05 18:17:53.326][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-06-05 18:17:53.328][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-06-05 18:17:53.330][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-06-05 18:17:53.332][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-06-05 18:17:53.334][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-06-05 18:17:53.336][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-06-05 18:17:53.338][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-06-05 18:17:53.340][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-06-05 18:17:53.342][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-06-05 18:17:53.344][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-06-05 18:17:53.346][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-06-05 18:17:53.348][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-06-05 18:17:53.350][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-06-05 18:17:53.352][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-06-05 18:17:53.354][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-06-05 18:17:53.356][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-06-05 18:17:53.358][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-06-05 18:17:53.360][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-06-05 18:17:53.362][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-06-05 18:17:53.364][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-06-05 18:17:53.366][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-06-05 18:17:53.368][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-06-05 18:17:53.370][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-06-05 18:17:53.372][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-06-05 18:17:53.374][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-06-05 18:17:53.400][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-06-05 18:17:53.402][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-06-05 18:17:53.405][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-06-05 18:17:53.407][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-06-05 18:17:53.409][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-06-05 18:17:53.411][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-06-05 18:17:53.413][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-06-05 18:17:53.414][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-06-05 18:17:53.416][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-06-05 18:17:53.418][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-06-05 18:17:53.420][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-06-05 18:17:53.422][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-06-05 18:17:53.424][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-06-05 18:17:53.426][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-06-05 18:17:53.428][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-06-05 18:17:53.430][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-06-05 18:17:53.432][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-06-05 18:17:53.434][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-06-05 18:17:53.436][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-06-05 18:17:53.438][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-06-05 18:17:53.440][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-06-05 18:17:53.442][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-06-05 18:17:53.444][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-06-05 18:17:53.446][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-06-05 18:17:53.448][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-06-05 18:17:53.450][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-06-05 18:17:53.452][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-06-05 18:17:53.453][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:17:53.454][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.457][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.493][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[2023-06-05 18:17:53.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.501][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[2023-06-05 18:17:53.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.562][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[2023-06-05 18:17:53.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.570][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[2023-06-05 18:17:53.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:53.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:53.623][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-06-05 18:17:53.625][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-06-05 18:17:53.628][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:53.630][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-06-05 18:17:53.631][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.633][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:53.635][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:53.636][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-06-05 18:17:53.638][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.639][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:53.641][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-06-05 18:17:53.642][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:53.644][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.645][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-06-05 18:17:53.647][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-06-05 18:17:53.648][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-06-05 18:17:53.650][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:53.652][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:17:53.652][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-06-05 18:17:53.652][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2023-06-05 18:17:53.653][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-06-05 18:17:53.655][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:53.656][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:53.657][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:53.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:53.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:53.662][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:53.663][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-06-05 18:17:53.663][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-06-05 18:17:53.665][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:53.666][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:53.668][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:53.669][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:53.671][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2023-06-05 18:17:53.673][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-06-05 18:17:53.676][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-06-05 18:17:53.678][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-06-05 18:17:53.681][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-06-05 18:17:53.685][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-06-05 18:17:53.687][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-06-05 18:17:53.689][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-06-05 18:17:53.691][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-06-05 18:17:53.693][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:53.694][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:53.711][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-06-05 18:17:53.713][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-06-05 18:17:53.714][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-06-05 18:17:53.714][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-06-05 18:17:53.716][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:53.718][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:53.719][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-06-05 18:17:53.720][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-06-05 18:17:53.722][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-06-05 18:17:53.724][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-06-05 18:17:53.726][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:53.727][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:53.729][private$addConnectorRules] Create new rule for URL "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-06-05 18:17:53.731][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-06-05 18:17:53.732][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-06-05 18:17:53.734][biodb::testThat]
biodb.INFO [2023-06-05 18:17:53.736][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2023-06-05 18:17:53.737][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:17:53.739][biodb::testThat]
biodb.DEBUG[2023-06-05 18:17:53.753][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-06-05 18:17:53.754][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2023-06-05 18:17:53.756][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2023-06-05 18:17:53.760][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:53.762][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:53.764][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-06-05 18:17:53.766][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:53.767][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-06-05 18:17:53.773][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-06-05 18:17:53.774][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-06-05 18:17:53.776][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-06-05 18:17:53.777][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-06-05 18:17:53.778][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-06-05 18:17:53.780][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2023-06-05 18:17:53.782][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-06-05 18:17:53.784][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-06-05 18:17:53.786][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:53.788][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-06-05 18:17:53.791][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-06-05 18:17:53.792][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-06-05 18:17:53.795][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-06-05 18:17:53.796][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-06-05 18:17:53.819][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-06-05 18:17:53.820][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-06-05 18:17:53.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:17:53.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:53.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:53.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:53.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:53.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:53.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:17:53.842][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:53.844][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:53.845][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.846][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:53.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:53.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.857][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:53.866][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:53.868][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.870][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.872][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:53.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:53.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.882][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:53.883][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:53.884][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.886][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.888][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:53.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:53.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.897][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:53.899][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:53.900][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.902][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.904][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:53.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:53.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.913][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:53.915][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:53.916][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.917][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:53.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:53.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.929][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:53.930][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:53.932][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.933][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:53.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:53.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.945][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:53.946][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:53.948][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.949][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.951][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:53.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:53.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.960][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:53.962][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:53.963][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.964][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.966][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:53.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:53.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.976][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:53.977][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:53.979][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.980][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.982][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:53.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:53.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.991][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:53.993][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:53.994][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:53.995][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:53.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:53.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:54.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.007][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:54.008][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:54.009][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.011][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.013][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:54.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:54.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.030][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:54.032][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:54.034][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.035][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.037][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:54.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:54.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.046][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.048][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.049][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.051][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.063][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.064][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.065][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.067][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.078][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:54.080][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:54.081][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.083][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:54.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:54.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.094][ef$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:54.095][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:54.096][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.098][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.100][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:54.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:54.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.109][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:54.110][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:54.112][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.113][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.115][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:54.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:54.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.125][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-06-05 18:17:54.126][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:54.127][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.129][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.131][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-06-05 18:17:54.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:54.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:54.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:54.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:54.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:54.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:54.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:54.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.157][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:54.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:54.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.163][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:54.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:54.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.169][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:54.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:54.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.183][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:54.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:54.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.189][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:54.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:54.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.195][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:54.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:54.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:54.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:54.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:54.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:54.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:54.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:54.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:54.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:54.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:54.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:54.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:54.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:54.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.236][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:54.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:54.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.241][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:54.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:54.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.247][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:54.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:54.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.253][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:54.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:54.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.259][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:54.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:54.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.264][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:54.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:54.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.270][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:54.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:54.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.276][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:54.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:54.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.282][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:54.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:54.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.288][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:54.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:54.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.293][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:54.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:54.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.299][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:54.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:54.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.305][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:54.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:54.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.311][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:54.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:54.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.316][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:54.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:54.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:54.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:54.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:54.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:54.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:54.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:54.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.366][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:54.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:54.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.371][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:54.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:54.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.377][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:54.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:54.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:54.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:54.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:54.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:54.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:54.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:54.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.418][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:54.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:54.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.424][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:54.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:54.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.430][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:54.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:54.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.436][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:54.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:54.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.442][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:54.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:54.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.448][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:54.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:54.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.454][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:54.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:54.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.460][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:54.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:54.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.466][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:54.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:54.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.472][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-06-05 18:17:54.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.492][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.504][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-06-05 18:17:54.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:54.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:54.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.520][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:54.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:54.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.526][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:54.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:54.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:54.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:54.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:54.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:54.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.547][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:54.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:54.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.553][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:54.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:54.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:54.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:54.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.564][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:54.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:54.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:54.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:54.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:54.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:54.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:54.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:54.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:54.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:54.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:54.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:54.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:54.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:54.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:54.608][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-06-05 18:17:54.610][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:54.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:54.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.616][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:54.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:54.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.621][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:54.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:54.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.627][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:54.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:54.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:54.641][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-06-05 18:17:54.643][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-06-05 18:17:54.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:17:54.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:54.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:54.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:54.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:54.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:54.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:54.661][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-06-05 18:17:54.662][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-06-05 18:17:54.665][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:54.667][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-06-05 18:17:54.669][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-06-05 18:17:54.671][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-06-05 18:17:54.673][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-06-05 18:17:54.675][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-06-05 18:17:54.697][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-06-05 18:17:54.699][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-06-05 18:17:54.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:17:54.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:54.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:54.712][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:54.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:54.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:54.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:17:54.720][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:54.721][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:54.723][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.724][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:54.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:54.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.735][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:54.737][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:54.738][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.740][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.741][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:54.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:54.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.751][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:54.752][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:54.754][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.755][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.757][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:54.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:54.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.767][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:54.768][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:54.770][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.771][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.773][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:54.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:54.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.782][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:54.792][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:54.793][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.795][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:54.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:54.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.807][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:54.808][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:54.810][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.811][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:54.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.822][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:54.824][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:54.825][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.827][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.829][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:54.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:54.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.838][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:54.840][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:54.841][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.842][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.844][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:54.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:54.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.854][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:54.855][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:54.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.858][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.860][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:54.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:54.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.869][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:54.871][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:54.872][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.873][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.875][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:54.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:54.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.885][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:54.886][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:54.888][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.889][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.891][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:54.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:54.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.900][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:54.902][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:54.903][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.904][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.906][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:54.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:54.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.916][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.917][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.919][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.920][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:54.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.931][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.933][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.934][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.936][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:54.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.956][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:54.957][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:54.959][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.960][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:54.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:54.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.971][ef$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:54.973][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:54.974][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.976][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.977][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:54.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:54.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.987][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:54.988][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:54.990][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.991][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:54.993][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:54.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:54.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:54.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.002][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-06-05 18:17:55.004][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:55.005][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.007][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.009][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-06-05 18:17:55.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:55.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:55.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:55.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:55.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:55.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:55.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:55.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.036][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:55.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:55.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.042][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:55.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:55.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.047][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:17:55.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:17:55.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.053][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:55.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:55.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.059][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:55.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:55.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.065][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-06-05 18:17:55.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-06-05 18:17:55.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:55.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:55.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:55.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:55.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:17:55.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:17:55.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:55.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:55.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:55.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:55.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:55.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-06-05 18:17:55.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.114][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:55.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:55.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.120][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:55.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:55.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.125][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:55.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:17:55.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.131][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:55.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:55.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.137][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:55.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:55.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.143][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:55.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-06-05 18:17:55.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.149][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:55.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:55.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.155][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:55.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:55.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.160][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:55.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-06-05 18:17:55.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.166][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.172][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.178][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.184][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:55.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:55.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.189][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:55.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:55.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.195][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:17:55.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:17:55.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:55.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:55.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.207][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:55.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:55.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-06-05 18:17:55.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-06-05 18:17:55.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.218][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.230][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.236][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:55.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:55.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.242][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:55.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:55.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.256][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:55.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:17:55.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:55.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:55.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:55.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:55.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:55.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:17:55.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:55.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:55.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:55.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:55.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:55.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:55.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.297][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:55.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:55.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.303][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:55.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:55.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.309][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:55.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:17:55.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.315][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:55.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:55.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.321][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:55.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:55.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.327][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:55.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-06-05 18:17:55.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.332][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:55.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:55.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.338][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:55.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:55.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.344][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-06-05 18:17:55.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-06-05 18:17:55.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.350][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-06-05 18:17:55.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.367][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.373][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-06-05 18:17:55.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-06-05 18:17:55.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.383][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:55.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:55.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:55.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:55.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:55.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:55.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:55.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:55.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:17:55.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:17:55.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.426][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:55.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:55.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.432][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:55.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:55.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:55.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:55.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.444][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:55.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:17:55.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:55.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:55.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:55.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:55.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:55.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:55.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:55.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:55.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:55.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:55.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:17:55.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:17:55.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:55.490][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-06-05 18:17:55.492][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.498][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.503][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.509][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:55.515][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-06-05 18:17:55.516][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2023-06-05 18:17:55.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:17:55.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:55.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:55.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:55.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:55.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:55.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:55.548][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-06-05 18:17:55.550][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-06-05 18:17:55.559][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-06-05 18:17:55.562][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:55.564][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:55.566][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-06-05 18:17:55.568][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:55.570][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-06-05 18:17:55.575][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-06-05 18:17:55.577][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-06-05 18:17:55.578][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-06-05 18:17:55.580][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-06-05 18:17:55.581][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-06-05 18:17:55.582][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-06-05 18:17:55.585][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.591][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.596][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.602][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.608][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.614][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.619][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:55.625][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-06-05 18:17:55.626][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-06-05 18:17:55.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:17:55.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:55.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:55.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:55.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:55.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:55.647][FUN] Functions in observer BiodbConfig: [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[2023-06-05 18:17:55.649][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.656][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.662][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.668][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.674][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.680][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.686][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:55.692][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-06-05 18:17:55.693][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-06-05 18:17:55.695][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:17:55.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:55.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:55.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:55.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:55.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:55.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:55.743][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-06-05 18:17:55.745][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-06-05 18:17:55.746][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-06-05 18:17:55.749][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:55.751][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:55.753][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-06-05 18:17:55.756][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-06-05 18:17:55.757][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-06-05 18:17:55.763][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-06-05 18:17:55.765][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-06-05 18:17:55.766][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-06-05 18:17:55.768][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-06-05 18:17:55.769][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-06-05 18:17:55.771][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-06-05 18:17:55.774][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.780][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.785][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.791][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.797][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.803][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.809][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:55.815][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-06-05 18:17:55.816][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2023-06-05 18:17:55.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:17:55.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:55.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:55.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:55.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:55.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:55.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:17:55.833][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.839][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.845][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.850][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.856][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.862][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:17:55.868][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-06-05 18:17:55.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-06-05 18:17:55.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:17:55.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:17:55.881][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-06-05 18:17:55.883][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-06-05 18:17:55.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:17:55.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:55.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:55.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:55.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:55.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:55.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-06-05 18:17:55.905][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-06-05 18:17:55.907][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-06-05 18:17:55.908][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-06-05 18:17:55.910][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-06-05 18:17:55.911][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:17:55.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:17:55.914][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:55.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:55.916][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:55.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 199 ]
>
> proc.time()
user system elapsed
13.124 0.386 17.756
biodbHmdb.Rcheck/biodbHmdb-Ex.timings
| name | user | system | elapsed | |
| HmdbMetabolitesConn | 0.714 | 0.060 | 0.776 | |
| HmdbMetabolitesEntry | 0.159 | 0.002 | 0.161 | |