| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:30 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 193/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbHmdb 1.7.0 (landing page) Pierrick Roger
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / 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: 2023-05-30 01:51:03 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 01:52:21 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 77.1 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 (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* 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++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* checking installed package size ... NOTE
installed size is 6.6Mb
sub-directories of 1Mb or more:
libs 6.0Mb
* 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++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ 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/site-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/site-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/site-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/site-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/site-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 [2023-05-30 01:51:52.658][biodb::testContext]
biodb.INFO [2023-05-30 01:51:52.661][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:51:52.662][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2023-05-30 01:51:52.664][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:51:52.665][biodb::testContext]
biodb.INFO [2023-05-30 01:51:52.667][biodb::testThat]
biodb.INFO [2023-05-30 01:51:52.668][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2023-05-30 01:51:52.669][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:51:52.671][biodb::testThat]
biodb.INFO [2023-05-30 01:51:52.801][biodb::testContext]
biodb.INFO [2023-05-30 01:51:52.803][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:51:52.804][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-05-30 01:51:52.806][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:51:52.807][biodb::testContext]
biodb.INFO [2023-05-30 01:51:52.828][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-30 01:51:52.830][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-30 01:51:52.839][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:51:52.841][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-30 01:51:52.842][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-30 01:51:52.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.847][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-30 01:51:52.872][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-30 01:51:52.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.878][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-30 01:51:52.879][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-30 01:51:52.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.884][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-30 01:51:52.885][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-30 01:51:52.887][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-30 01:51:52.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.891][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-30 01:51:52.893][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-30 01:51:52.894][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-30 01:51:52.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.899][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-30 01:51:52.900][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-30 01:51:52.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.904][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[2023-05-30 01:51:52.905][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-30 01:51:52.907][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-30 01:51:52.908][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-30 01:51:52.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.913][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-30 01:51:52.914][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-30 01:51:52.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.919][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-30 01:51:52.920][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-30 01:51:52.922][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-30 01:51:52.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.926][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-30 01:51:52.928][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-30 01:51:52.939][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-30 01:51:52.941][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-30 01:51:52.942][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-30 01:51:52.943][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-30 01:51:52.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.948][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-30 01:51:52.950][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-30 01:51:52.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.955][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-30 01:51:52.956][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-30 01:51:52.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.961][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-30 01:51:52.963][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-30 01:51:52.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.968][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-30 01:51:52.969][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-30 01:51:52.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.974][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-30 01:51:52.976][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-30 01:51:52.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.981][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-30 01:51:52.982][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-30 01:51:52.986][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-30 01:51:52.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:52.991][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-30 01:51:52.993][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-30 01:51:52.994][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-30 01:51:52.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:52.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:52.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.003][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-30 01:51:53.049][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.071][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-30 01:51:53.073][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.074][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:51:53.076][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.077][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.078][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.080][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.081][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:51:53.082][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:51:53.084][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.085][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-30 01:51:53.086][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:51:53.088][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.089][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.091][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:51:53.091][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:51:53.091][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-30 01:51:53.091][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-30 01:51:53.091][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-30 01:51:53.092][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:51:53.093][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:51:53.094][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:51:53.096][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:51:53.097][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:51:53.098][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:51:53.099][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.101][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.102][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:51:53.103][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:51:53.105][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.106][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.108][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-30 01:51:53.110][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.111][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-30 01:51:53.113][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.114][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:51:53.115][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.117][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.118][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.119][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.121][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-30 01:51:53.122][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:51:53.123][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.125][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-30 01:51:53.126][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:51:53.127][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.129][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.130][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:51:53.130][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:51:53.130][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-30 01:51:53.130][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-30 01:51:53.130][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-30 01:51:53.131][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:51:53.133][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:51:53.134][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:51:53.135][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:51:53.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:51:53.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:51:53.139][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.140][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.142][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:51:53.143][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:51:53.144][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.145][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.147][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-30 01:51:53.149][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.151][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-30 01:51:53.152][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.153][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:51:53.155][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.156][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.158][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.159][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.160][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:51:53.161][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:51:53.163][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.164][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-30 01:51:53.166][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:51:53.167][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.168][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.170][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.179][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:51:53.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:51:53.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:51:53.183][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:51:53.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:51:53.185][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:51:53.187][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.188][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.189][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:51:53.191][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:51:53.192][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.193][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.195][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-30 01:51:53.197][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.199][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-30 01:51:53.200][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.201][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:51:53.203][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.204][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.205][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.207][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.208][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-30 01:51:53.210][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:51:53.211][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.212][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-30 01:51:53.214][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:51:53.215][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.216][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.218][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.219][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:51:53.221][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:51:53.222][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:51:53.223][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:51:53.224][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:51:53.226][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:51:53.227][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.228][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.230][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:51:53.231][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:51:53.232][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.234][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.239][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:51:53.240][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.347][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-30 01:51:53.353][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-30 01:51:53.355][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-30 01:51:53.357][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-30 01:51:53.359][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-30 01:51:53.361][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-30 01:51:53.363][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-30 01:51:53.365][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-30 01:51:53.367][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-30 01:51:53.369][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-30 01:51:53.370][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-30 01:51:53.372][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-30 01:51:53.374][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-30 01:51:53.376][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-30 01:51:53.378][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-30 01:51:53.380][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-30 01:51:53.382][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-30 01:51:53.384][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-30 01:51:53.386][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-30 01:51:53.388][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-30 01:51:53.390][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-30 01:51:53.392][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-30 01:51:53.394][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-30 01:51:53.396][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-30 01:51:53.398][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-30 01:51:53.400][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-30 01:51:53.401][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-30 01:51:53.403][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-30 01:51:53.405][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-30 01:51:53.407][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-30 01:51:53.409][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-30 01:51:53.411][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-30 01:51:53.420][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-30 01:51:53.423][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-30 01:51:53.425][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-30 01:51:53.426][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-30 01:51:53.428][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-30 01:51:53.430][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-30 01:51:53.432][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-30 01:51:53.434][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-30 01:51:53.436][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-30 01:51:53.438][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-30 01:51:53.440][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-30 01:51:53.442][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-30 01:51:53.444][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-30 01:51:53.446][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-30 01:51:53.448][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-30 01:51:53.450][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-30 01:51:53.452][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-30 01:51:53.454][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-30 01:51:53.456][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-30 01:51:53.458][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-30 01:51:53.460][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-30 01:51:53.462][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-30 01:51:53.464][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-30 01:51:53.466][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-30 01:51:53.468][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-30 01:51:53.470][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-30 01:51:53.472][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-30 01:51:53.474][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-30 01:51:53.476][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-30 01:51:53.478][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-30 01:51:53.480][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-30 01:51:53.482][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-30 01:51:53.484][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-30 01:51:53.486][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-30 01:51:53.488][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-30 01:51:53.490][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-30 01:51:53.492][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-30 01:51:53.494][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-30 01:51:53.495][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-30 01:51:53.498][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-30 01:51:53.499][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-30 01:51:53.501][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-30 01:51:53.503][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-30 01:51:53.505][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-30 01:51:53.507][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-30 01:51:53.509][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-30 01:51:53.511][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-30 01:51:53.513][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-30 01:51:53.515][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-30 01:51:53.517][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-30 01:51:53.519][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-30 01:51:53.527][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-30 01:51:53.529][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-30 01:51:53.534][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:51:53.535][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.538][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.553][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[2023-05-30 01:51:53.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.562][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[2023-05-30 01:51:53.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.579][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[2023-05-30 01:51:53.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:51:53.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:51:53.731][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-05-30 01:51:53.744][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-05-30 01:51:53.747][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.748][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.750][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.751][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:51:53.752][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.754][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-05-30 01:51:53.755][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.756][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.758][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-05-30 01:51:53.759][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:51:53.761][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.762][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-05-30 01:51:53.763][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-05-30 01:51:53.765][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-05-30 01:51:53.766][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-30 01:51:53.768][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:51:53.768][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-05-30 01:51:53.768][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2023-05-30 01:51:53.769][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-05-30 01:51:53.771][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:51:53.772][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:51:53.773][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:51:53.775][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:51:53.776][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:51:53.777][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:51:53.778][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-05-30 01:51:53.778][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-05-30 01:51:53.780][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:51:53.781][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:51:53.782][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-30 01:51:53.784][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:51:53.792][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2023-05-30 01:51:53.794][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-30 01:51:53.796][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-30 01:51:53.798][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-30 01:51:53.801][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-30 01:51:53.831][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-05-30 01:51:53.833][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-05-30 01:51:53.838][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-05-30 01:51:53.843][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-05-30 01:51:53.849][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:51:53.850][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:51:53.852][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-05-30 01:51:53.853][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-05-30 01:51:53.855][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-05-30 01:51:53.855][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-05-30 01:51:53.856][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:51:53.857][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:51:53.859][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-05-30 01:51:53.860][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-05-30 01:51:53.861][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-05-30 01:51:53.885][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-05-30 01:51:53.887][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:51:53.888][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:51:53.890][private$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[2023-05-30 01:51:53.891][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:51:53.893][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-05-30 01:51:53.913][biodb::testThat]
biodb.INFO [2023-05-30 01:51:53.914][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-05-30 01:51:53.915][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:51:53.917][biodb::testThat]
biodb.TRACE[2023-05-30 01:51:53.933][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[2023-05-30 01:51:53.940][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-05-30 01:51:53.945][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-05-30 01:51:53.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:51:53.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:53.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:53.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:53.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:53.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:53.970][FUN] Functions in observer BiodbConfig: [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[2023-05-30 01:51:53.985][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:53.986][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:53.987][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:53.989][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:53.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.017][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:54.018][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:54.019][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.021][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.057][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:54.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:54.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.067][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:54.068][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:54.069][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.071][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.073][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:54.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:54.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.082][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:54.083][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:54.084][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.086][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.087][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:54.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:54.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.096][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:54.098][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:54.099][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.100][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:54.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:54.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.111][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:54.113][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:54.114][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.115][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:54.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:54.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.126][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:54.128][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:54.129][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.130][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.132][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:54.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:54.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.150][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:54.152][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:54.153][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.154][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.156][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:54.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:54.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.166][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:54.167][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:54.168][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.170][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.172][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:54.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:54.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.181][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:54.183][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:54.184][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.185][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.187][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:54.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:54.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.196][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:54.198][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:54.199][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.200][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.202][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:54.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:54.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.211][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:54.213][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:54.214][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.215][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:54.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:54.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.227][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.228][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.230][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.231][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.242][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:54.243][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:54.245][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.246][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:54.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:54.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.257][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:54.259][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:54.260][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.261][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.263][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:54.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:54.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.272][ef$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:54.274][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:54.275][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.276][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.278][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:54.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:54.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.288][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:54.289][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:54.291][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.292][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.294][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:54.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:54.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.303][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-05-30 01:51:54.304][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:54.306][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.307][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.309][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-05-30 01:51:54.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:54.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.389][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:54.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:54.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.394][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:54.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:54.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.399][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:54.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:54.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.405][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:54.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:54.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.410][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:54.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:54.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.416][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:54.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:54.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:54.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:54.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:54.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:54.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:54.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:54.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:54.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:54.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:54.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:54.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:54.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:54.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.453][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:54.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:54.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.458][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:54.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:54.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.463][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:54.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:54.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.469][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:54.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:54.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.474][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:54.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:54.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.479][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:54.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:54.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.485][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:54.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:54.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.490][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:54.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:54.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.495][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:54.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:54.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.501][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:54.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:54.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.506][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:54.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:54.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.511][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:54.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:54.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.517][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:54.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:54.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.522][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:54.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:54.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.534][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:54.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:54.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:54.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:54.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:54.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:54.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:54.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:54.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.556][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.562][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.573][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:54.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:54.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.579][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:54.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:54.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.584][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:54.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:54.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:54.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:54.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:54.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:54.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:54.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:54.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.606][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:54.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:54.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.612][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:54.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:54.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:54.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:54.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.623][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:54.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:54.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.628][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:54.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:54.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.634][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:54.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:54.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.639][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:54.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:54.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.644][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:54.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:54.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.650][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:54.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:54.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.655][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:54.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:54.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.661][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:54.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:54.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.666][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:54.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:54.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.672][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-05-30 01:51:54.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.677][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.688][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.693][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-05-30 01:51:54.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:54.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:54.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:54.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.739][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:54.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:54.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.745][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:54.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:54.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:54.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:54.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.755][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:54.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:54.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.764][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.770][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.781][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:51:54.823][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2023-05-30 01:51:54.830][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:51:54.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:51:54.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.836][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:51:54.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:51:54.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.841][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-30 01:51:54.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-30 01:51:54.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.847][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-30 01:51:54.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-30 01:51:54.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.883][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.937][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.943][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.949][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:54.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.982][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.983][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.985][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.986][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:54.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:54.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:54.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:54.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.003][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:55.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:55.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.009][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:55.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:55.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.014][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:55.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:55.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.020][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:55.021][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:55.023][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.024][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.025][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:55.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:55.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:55.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:55.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:55.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:55.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:55.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:55.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.057][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:55.059][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:55.060][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.061][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:55.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:55.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.078][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:55.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:55.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.084][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:55.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:55.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.089][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:55.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:55.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.095][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:55.096][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:55.097][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.099][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.100][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:55.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:55.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:55.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:55.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:55.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:55.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:55.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:55.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.139][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:55.141][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:55.142][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.143][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:55.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:55.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.160][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:55.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:55.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.166][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:55.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:55.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.171][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:55.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:55.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.177][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:55.178][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:55.180][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.181][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.182][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:55.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:55.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:55.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:55.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.203][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:55.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:55.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.209][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:55.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:55.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.214][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:55.216][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:55.217][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.218][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.220][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:55.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:55.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.235][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:55.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:55.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.241][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:55.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:55.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.246][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:55.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:55.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.252][ef$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:55.254][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:55.255][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.256][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.258][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:55.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:55.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.273][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:55.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:55.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.278][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:55.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:55.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.284][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:55.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:55.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.290][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:55.291][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:55.292][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.294][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:55.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:55.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.310][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:55.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:55.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.323][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:55.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:55.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.328][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:55.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:55.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.334][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:55.335][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:55.337][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.338][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.339][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:55.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:55.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:55.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:55.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:55.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:55.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:55.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:55.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.372][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:55.373][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:55.375][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.376][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:55.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:55.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.393][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:55.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:55.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.399][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:55.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:55.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.404][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:55.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:55.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.410][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:55.411][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:55.413][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.414][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.415][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:55.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:55.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.431][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:55.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:55.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.437][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:55.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:55.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.442][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:55.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:55.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.448][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:55.449][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:55.451][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.452][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.453][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:55.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:55.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.469][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:55.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:55.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.475][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:55.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:55.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.480][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:55.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:55.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.486][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:55.487][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:55.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.490][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.491][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:55.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:55.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.507][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:55.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:55.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.519][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:55.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:55.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.525][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:55.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:55.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.531][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:55.532][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:55.533][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.535][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.536][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:55.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:55.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.552][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:55.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:55.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:55.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:55.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:55.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:55.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.569][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:55.571][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:55.572][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.573][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:55.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:55.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:55.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:55.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:55.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:55.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.602][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:55.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:55.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.607][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:55.609][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:55.610][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.611][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.613][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:55.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:55.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.628][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:55.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:55.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.634][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:55.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:55.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.639][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:55.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:55.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.645][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:55.646][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:55.647][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.649][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.650][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:55.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:55.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.665][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:55.667][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:55.668][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.669][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.677][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:55.679][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:55.680][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.681][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.689][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:55.691][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:55.692][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.693][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.701][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:55.702][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:55.711][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.712][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.720][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:55.721][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:55.723][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.724][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.732][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:55.733][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:55.735][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.736][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.744][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:55.746][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:55.747][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.748][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.756][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:55.758][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:55.759][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.760][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.768][ef$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:55.770][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:55.771][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.773][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.780][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:55.782][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:55.783][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.785][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.793][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:55.794][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:55.796][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.797][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.805][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:55.807][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:55.808][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.809][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.817][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:55.819][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:55.820][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.821][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.829][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:55.831][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:55.832][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.834][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.842][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:55.843][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:55.845][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.846][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.854][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:55.856][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:55.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.858][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.866][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:55.868][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:55.869][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.870][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:55.878][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:55.880][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:55.881][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:55.883][ef$get] fields variable is a list.
biodb.INFO [2023-05-30 01:51:55.892][biodb::testThat]
biodb.INFO [2023-05-30 01:51:55.893][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-05-30 01:51:55.895][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:51:55.896][biodb::testThat]
biodb.DEBUG[2023-05-30 01:51:55.923][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-05-30 01:51:55.933][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-05-30 01:51:55.940][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:51:55.942][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-05-30 01:51:55.945][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-05-30 01:51:55.947][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-30 01:51:55.951][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-05-30 01:51:55.953][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-05-30 01:51:56.013][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-05-30 01:51:56.014][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-05-30 01:51:56.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:51:56.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:51:56.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:51:56.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:51:56.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:51:56.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:51:56.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:51:56.035][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:56.037][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:56.038][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.039][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:56.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:56.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.050][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:56.052][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:56.053][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.055][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.057][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:56.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:56.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.066][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:56.067][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:56.069][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.070][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.072][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:56.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:56.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.081][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:56.083][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:56.084][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.085][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.087][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:56.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:56.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.105][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:56.107][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:56.108][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.109][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:56.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:56.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.120][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:56.122][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:56.123][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.124][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:56.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:56.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.136][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:56.137][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:56.139][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.140][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.142][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:56.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:56.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.151][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:56.153][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:56.154][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.155][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.157][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:56.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:56.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.166][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:56.168][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:56.169][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.171][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.173][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:56.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:56.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.182][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:56.183][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:56.185][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.186][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.188][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:56.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:56.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.197][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:56.199][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:56.200][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.202][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.203][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:56.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:56.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.216][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:56.219][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:56.220][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.222][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:56.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:56.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.236][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.237][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.239][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.240][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.252][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:56.254][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:56.255][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.257][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:56.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:56.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.268][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.270][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.271][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.273][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.284][ef$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:56.286][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:56.287][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.289][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.290][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:56.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:56.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.300][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:56.301][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:56.303][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.318][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.321][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:56.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:56.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.330][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-05-30 01:51:56.332][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:56.333][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.335][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.337][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-05-30 01:51:56.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:56.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:56.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:56.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:56.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:56.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:56.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:56.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.365][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:56.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:56.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.371][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:56.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:56.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.377][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:51:56.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:51:56.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.383][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:56.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:56.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.389][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:56.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:56.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.395][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:51:56.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:51:56.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:56.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:56.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:56.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:56.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:51:56.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:51:56.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:56.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:56.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:56.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:56.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:56.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:51:56.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.436][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:56.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:56.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.442][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:56.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:56.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.448][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:56.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:51:56.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.453][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:56.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:56.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.459][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:56.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:56.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.464][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:56.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:51:56.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.470][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:56.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:56.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.476][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:56.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:56.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.481][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:56.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:51:56.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.487][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:56.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:56.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.493][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:56.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:56.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.498][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:56.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:56.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.504][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:56.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:56.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.517][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:56.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:56.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.523][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:51:56.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:51:56.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:56.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:56.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.534][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:56.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:56.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:51:56.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:51:56.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.562][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:56.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:56.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.568][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:56.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:56.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.573][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:56.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:51:56.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:56.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:56.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:56.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:56.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:56.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:51:56.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.596][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.601][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.613][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:56.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:56.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.618][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:56.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:56.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.624][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:56.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:51:56.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.630][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:56.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:56.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.635][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:56.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:56.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.641][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:56.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:56.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.646][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:56.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:56.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.652][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:56.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:56.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.657][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:51:56.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:51:56.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.663][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-05-30 01:51:56.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.674][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.680][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.685][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-05-30 01:51:56.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:51:56.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.720][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.735][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:56.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:56.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.741][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:56.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:56.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:56.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:56.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.752][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:56.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:51:56.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:56.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:56.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:56.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:56.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:56.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:56.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:56.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:56.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:56.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:56.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:51:56.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:51:56.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:51:56.795][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-05-30 01:51:56.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-05-30 01:51:56.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-05-30 01:51:56.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-05-30 01:51:56.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-05-30 01:51:56.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-05-30 01:51:56.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-05-30 01:51:56.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-30 01:51:56.821][biodb::testThat]
biodb.INFO [2023-05-30 01:51:56.823][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-05-30 01:51:56.824][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:51:56.825][biodb::testThat]
biodb.TRACE[2023-05-30 01:51:56.829][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.831][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.832][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.834][ef$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:51:56.835][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2023-05-30 01:51:56.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.888][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:51:56.901][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2023-05-30 01:51:56.913][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-05-30 01:51:56.915][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-05-30 01:51:56.916][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-05-30 01:51:56.918][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:51:56.920][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:51:56.922][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-05-30 01:51:56.924][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:51:56.926][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-05-30 01:51:56.931][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-05-30 01:51:56.933][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-05-30 01:51:56.934][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-05-30 01:51:56.936][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-05-30 01:51:56.937][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-05-30 01:51:56.939][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-05-30 01:51:56.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:56.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:56.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:56.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:51:56.964][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-05-30 01:51:56.965][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-05-30 01:51:56.966][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2023-05-30 01:51:56.986][ef$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:56.988][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:56.989][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:56.990][ef$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:51:56.992][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2023-05-30 01:51:57.012][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:57.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:57.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.018][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:57.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:57.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.023][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:57.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:57.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:51:57.030][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[2023-05-30 01:51:57.123][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-05-30 01:51:57.124][private$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[2023-05-30 01:51:57.126][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2023-05-30 01:51:57.146][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:51:57.148][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:51:57.150][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-05-30 01:51:57.151][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:51:57.153][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-05-30 01:51:57.178][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-05-30 01:51:57.179][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-05-30 01:51:57.181][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-05-30 01:51:57.182][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-05-30 01:51:57.183][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-05-30 01:51:57.185][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-05-30 01:51:57.187][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:57.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:57.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.192][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:57.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:57.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.198][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:57.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:57.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.203][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:51:57.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:51:57.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:51:57.208][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-05-30 01:51:57.210][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-05-30 01:51:57.211][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2023-05-30 01:51:57.238][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.240][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.241][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.242][ef$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:51:57.244][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2023-05-30 01:51:57.264][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.270][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.275][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:51:57.283][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2023-05-30 01:51:57.295][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2023-05-30 01:51:57.296][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2023-05-30 01:51:57.298][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2023-05-30 01:51:57.300][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:51:57.302][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:51:57.304][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-05-30 01:51:57.306][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:51:57.307][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-05-30 01:51:57.312][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-05-30 01:51:57.314][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-05-30 01:51:57.315][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-05-30 01:51:57.316][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-05-30 01:51:57.318][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-05-30 01:51:57.319][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-05-30 01:51:57.322][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.327][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.333][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.338][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:51:57.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:51:57.344][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-05-30 01:51:57.345][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-05-30 01:51:57.346][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2023-05-30 01:51:57.367][biodb::testThat]
biodb.INFO [2023-05-30 01:51:57.369][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-05-30 01:51:57.370][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:51:57.371][biodb::testThat]
biodb.TRACE[2023-05-30 01:51:57.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:57.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:57.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:57.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:57.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:57.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:57.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:51:57.441][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-05-30 01:51:57.442][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-05-30 01:51:57.443][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-05-30 01:51:57.446][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:51:57.447][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:51:57.449][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-05-30 01:51:57.451][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:51:57.452][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-05-30 01:51:57.458][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-05-30 01:51:57.459][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-05-30 01:51:57.460][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-05-30 01:51:57.462][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-05-30 01:51:57.463][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-05-30 01:51:57.464][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-05-30 01:51:57.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:57.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:57.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:57.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:57.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:57.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:57.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:51:57.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:51:57.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:51:57.488][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-05-30 01:51:57.489][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2023-05-30 01:51:57.510][biodb::testThat]
biodb.INFO [2023-05-30 01:51:57.511][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-05-30 01:51:57.513][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:51:57.514][biodb::testThat]
biodb.TRACE[2023-05-30 01:51:57.548][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:51:57.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:51:57.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.554][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:51:57.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:51:57.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.559][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-30 01:51:57.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-30 01:51:57.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.564][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-30 01:51:57.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-30 01:51:57.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.637][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:51:57.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:51:57.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.643][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-30 01:51:57.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-30 01:51:57.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.648][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-30 01:51:57.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-30 01:51:57.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:51:57.653][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-30 01:51:57.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-30 01:51:57.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:51:57.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-30 01:51:57.662][biodb::testThat]
biodb.INFO [2023-05-30 01:51:57.663][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-05-30 01:51:57.665][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:51:57.666][biodb::testThat]
biodb.INFO [2023-05-30 01:51:57.672][biodb::testThat]
biodb.INFO [2023-05-30 01:51:57.673][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-05-30 01:51:57.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:51:57.676][biodb::testThat]
biodb.INFO [2023-05-30 01:51:57.682][biodb::testThat]
biodb.INFO [2023-05-30 01:51:57.683][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-05-30 01:51:57.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:51:57.686][biodb::testThat]
biodb.DEBUG[2023-05-30 01:51:57.690][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2023-05-30 01:52:01.632][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2023-05-30 01:52:02.135][biodb::testThat]
biodb.INFO [2023-05-30 01:52:02.136][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-05-30 01:52:02.138][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:02.139][biodb::testThat]
biodb.DEBUG[2023-05-30 01:52:03.779][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2023-05-30 01:52:04.280][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:04.349][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:04.355][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.357][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.358][ef$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:04.360][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:04.361][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.363][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.364][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:04.366][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:04.368][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.369][ef$get] fields variable is a list.
biodb.INFO [2023-05-30 01:52:04.371][biodb::testThat]
biodb.INFO [2023-05-30 01:52:04.373][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-05-30 01:52:04.374][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:04.376][biodb::testThat]
biodb.DEBUG[2023-05-30 01:52:04.379][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-05-30 01:52:04.451][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2023-05-30 01:52:04.453][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2023-05-30 01:52:04.455][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2023-05-30 01:52:04.457][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2023-05-30 01:52:04.458][private$doDownload] Downloading HMDB metabolite database at "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2023-05-30 01:52:04.461][cch$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2023-05-30 01:52:04.463][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2023-05-30 01:52:04.466][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2023-05-30 01:52:04.468][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2023-05-30 01:52:04.470][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2023-05-30 01:52:04.472][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/markerbeae799c5535marker".
biodb.TRACE[2023-05-30 01:52:04.474][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2023-05-30 01:52:04.476][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-05-30 01:52:04.478][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2023-05-30 01:52:04.480][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2023-05-30 01:52:04.481][private$doExtractDownload] Extracting content of downloaded',
' HMDB metabolite database...
biodb.DEBUG[2023-05-30 01:52:04.483][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2023-05-30 01:52:04.485][private$doExtractDownload] Unzipping /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /home/biocbuild/.cache/R/biodb/tmp...
biodb.DEBUG[2023-05-30 01:52:04.488][private$findXmlDatabaseFile] Found files [1]: "hmdb_two_full_entries.xml" into /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2023-05-30 01:52:04.489][private$findXmlDatabaseFile] Found XML file /home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2023-05-30 01:52:04.490][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2023-05-30 01:52:04.493][private$doExtractDownload] Extract entries from XML file "/home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2023-05-30 01:52:04.501][self$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[2023-05-30 01:52:04.503][private$doAddFilesToCache] Destination files are [2]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-05-30 01:52:04.512][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-05-30 01:52:04.514][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2023-05-30 01:52:04.517][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/markerbeae732b90b7emarker".
biodb.TRACE[2023-05-30 01:52:04.518][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2023-05-30 01:52:04.520][self$addFilesToCache] Done adding files.
biodb.TRACE[2023-05-30 01:52:04.543][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-05-30 01:52:04.545][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-30 01:52:04.546][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-30 01:52:04.548][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-05-30 01:52:04.550][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:04.574][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-05-30 01:52:04.576][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-05-30 01:52:04.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:52:04.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:04.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:04.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:04.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:04.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:04.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:52:04.596][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:04.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:04.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.602][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:04.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:04.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:04.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:04.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:04.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:04.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:04.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:04.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:04.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:04.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:04.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:04.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:04.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:04.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:04.643][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-05-30 01:52:04.644][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-05-30 01:52:04.674][biodb::testThat]
biodb.INFO [2023-05-30 01:52:04.676][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-05-30 01:52:04.677][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:04.679][biodb::testThat]
biodb.DEBUG[2023-05-30 01:52:04.689][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2023-05-30 01:52:04.691][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2023-05-30 01:52:04.692][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-05-30 01:52:04.695][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:04.697][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-05-30 01:52:04.699][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2023-05-30 01:52:04.701][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-30 01:52:04.703][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-30 01:52:04.705][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-05-30 01:52:04.707][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:04.734][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-05-30 01:52:04.736][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-05-30 01:52:04.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:52:04.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:04.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:04.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:04.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:04.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:04.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:52:04.758][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:04.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:04.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.764][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:04.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:04.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:04.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:04.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:04.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:04.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:04.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:04.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:04.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:04.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:04.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:04.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:04.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:04.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:04.803][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-05-30 01:52:04.804][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-05-30 01:52:04.806][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2023-05-30 01:52:04.831][biodb::testThat]
biodb.INFO [2023-05-30 01:52:04.832][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-05-30 01:52:04.834][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:04.835][biodb::testThat]
biodb.INFO [2023-05-30 01:52:04.863][biodb::testThat]
biodb.INFO [2023-05-30 01:52:04.865][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-05-30 01:52:04.866][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:04.867][biodb::testThat]
biodb.DEBUG[2023-05-30 01:52:04.871][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:04.873][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:04.875][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-05-30 01:52:04.877][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:04.878][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-05-30 01:52:04.883][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-05-30 01:52:04.885][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-05-30 01:52:04.886][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-05-30 01:52:04.888][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2023-05-30 01:52:04.896][biodb::testThat]
biodb.INFO [2023-05-30 01:52:04.898][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-05-30 01:52:04.899][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:04.900][biodb::testThat]
biodb.DEBUG[2023-05-30 01:52:04.904][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:04.906][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:04.908][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-05-30 01:52:04.910][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:04.911][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-05-30 01:52:04.917][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-05-30 01:52:04.918][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-05-30 01:52:04.919][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-05-30 01:52:04.921][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2023-05-30 01:52:04.937][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:04.939][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:04.940][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.942][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.943][ef$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:04.944][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:04.946][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.947][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:04.948][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:04.950][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:04.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:04.952][ef$get] fields variable is a list.
biodb.INFO [2023-05-30 01:52:04.954][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-30 01:52:04.955][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-05-30 01:52:04.967][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-05-30 01:52:04.976][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-30 01:52:04.977][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:04.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:04.980][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:04.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:04.982][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:04.983][FUN] Functions in observer BiodbConfig: [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 [2023-05-30 01:52:04.989][biodb::testContext]
biodb.INFO [2023-05-30 01:52:04.990][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:52:04.991][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2023-05-30 01:52:04.993][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:52:04.994][biodb::testContext]
biodb.INFO [2023-05-30 01:52:05.003][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-30 01:52:05.005][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-30 01:52:05.010][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:52:05.011][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-30 01:52:05.013][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-30 01:52:05.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.018][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-30 01:52:05.019][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-30 01:52:05.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.024][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-30 01:52:05.026][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-30 01:52:05.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.031][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-30 01:52:05.032][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-30 01:52:05.034][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-30 01:52:05.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.037][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[2023-05-30 01:52:05.038][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-30 01:52:05.040][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-30 01:52:05.041][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-30 01:52:05.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.046][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-30 01:52:05.048][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-30 01:52:05.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.051][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[2023-05-30 01:52:05.053][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-30 01:52:05.054][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-30 01:52:05.056][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-30 01:52:05.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.061][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-30 01:52:05.062][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-30 01:52:05.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.066][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[2023-05-30 01:52:05.067][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-30 01:52:05.068][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-30 01:52:05.070][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-30 01:52:05.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.075][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-30 01:52:05.076][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-30 01:52:05.078][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-30 01:52:05.079][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-30 01:52:05.080][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-30 01:52:05.082][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-30 01:52:05.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.087][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-30 01:52:05.088][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-30 01:52:05.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.093][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-30 01:52:05.095][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-30 01:52:05.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.099][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-30 01:52:05.101][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-30 01:52:05.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.106][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-30 01:52:05.107][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-30 01:52:05.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.112][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-30 01:52:05.114][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-30 01:52:05.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.127][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-30 01:52:05.129][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-30 01:52:05.133][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-30 01:52:05.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.138][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-30 01:52:05.140][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-30 01:52:05.141][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-30 01:52:05.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.146][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-30 01:52:05.149][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.150][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-30 01:52:05.152][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.153][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:05.155][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.156][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.157][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.159][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.160][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:52:05.161][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:05.163][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.164][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-30 01:52:05.166][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:05.167][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.168][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.170][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:52:05.170][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:52:05.170][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-30 01:52:05.170][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-30 01:52:05.170][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-30 01:52:05.171][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:52:05.172][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:05.174][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:05.175][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:05.176][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:05.178][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:05.179][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.180][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.182][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:05.183][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:05.184][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.185][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.187][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-30 01:52:05.189][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.191][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-30 01:52:05.192][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.194][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:05.195][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.196][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.198][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.199][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.200][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-30 01:52:05.202][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:05.203][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.204][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-30 01:52:05.206][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:05.207][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.209][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.210][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:52:05.210][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:52:05.210][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-30 01:52:05.210][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-30 01:52:05.210][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-30 01:52:05.211][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:52:05.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:05.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:05.215][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:05.217][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:05.218][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:05.219][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.221][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.222][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:05.223][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:05.224][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.226][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.227][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-30 01:52:05.230][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.231][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-30 01:52:05.233][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.234][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:05.235][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.237][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.238][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.239][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.241][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:52:05.242][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:05.243][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.245][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-30 01:52:05.246][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:05.248][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.249][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.250][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.252][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:52:05.253][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:05.254][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:05.256][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:05.257][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:05.258][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:05.259][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.261][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.262][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:05.263][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:05.265][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.266][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.268][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-30 01:52:05.278][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.280][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-30 01:52:05.281][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.282][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:05.284][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.285][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.287][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.288][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.289][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-30 01:52:05.291][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:05.292][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.294][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-30 01:52:05.295][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:05.296][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.298][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.299][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.301][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:52:05.302][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:05.303][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:05.305][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:05.306][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:05.307][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:05.308][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.310][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.311][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:05.312][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:05.314][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.315][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.317][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:52:05.318][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.350][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[2023-05-30 01:52:05.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.356][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[2023-05-30 01:52:05.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.362][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[2023-05-30 01:52:05.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.381][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[2023-05-30 01:52:05.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.425][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[2023-05-30 01:52:05.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.432][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[2023-05-30 01:52:05.433][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-30 01:52:05.435][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-30 01:52:05.437][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-30 01:52:05.439][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-30 01:52:05.441][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-30 01:52:05.443][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-30 01:52:05.445][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-30 01:52:05.447][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-30 01:52:05.449][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-30 01:52:05.451][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-30 01:52:05.453][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-30 01:52:05.455][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-30 01:52:05.457][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-30 01:52:05.459][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-30 01:52:05.461][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-30 01:52:05.463][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-30 01:52:05.464][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-30 01:52:05.466][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-30 01:52:05.468][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-30 01:52:05.470][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-30 01:52:05.472][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-30 01:52:05.474][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-30 01:52:05.476][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-30 01:52:05.478][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-30 01:52:05.480][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-30 01:52:05.482][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-30 01:52:05.484][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-30 01:52:05.486][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-30 01:52:05.488][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-30 01:52:05.490][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-30 01:52:05.492][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-30 01:52:05.494][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-30 01:52:05.496][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-30 01:52:05.498][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-30 01:52:05.499][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-30 01:52:05.501][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-30 01:52:05.503][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-30 01:52:05.505][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-30 01:52:05.507][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-30 01:52:05.509][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-30 01:52:05.511][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-30 01:52:05.513][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-30 01:52:05.515][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-30 01:52:05.517][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-30 01:52:05.519][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-30 01:52:05.521][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-30 01:52:05.523][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-30 01:52:05.525][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-30 01:52:05.526][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-30 01:52:05.528][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-30 01:52:05.530][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-30 01:52:05.532][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-30 01:52:05.534][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-30 01:52:05.536][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-30 01:52:05.538][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-30 01:52:05.540][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-30 01:52:05.542][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-30 01:52:05.544][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-30 01:52:05.546][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-30 01:52:05.548][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-30 01:52:05.550][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-30 01:52:05.551][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-30 01:52:05.553][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-30 01:52:05.555][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-30 01:52:05.599][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-30 01:52:05.602][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-30 01:52:05.604][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-30 01:52:05.606][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-30 01:52:05.608][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-30 01:52:05.611][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-30 01:52:05.613][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-30 01:52:05.615][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-30 01:52:05.617][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-30 01:52:05.619][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-30 01:52:05.621][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-30 01:52:05.623][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-30 01:52:05.625][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-30 01:52:05.627][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-30 01:52:05.629][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-30 01:52:05.631][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-30 01:52:05.633][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-30 01:52:05.635][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-30 01:52:05.637][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-30 01:52:05.640][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-30 01:52:05.642][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-30 01:52:05.643][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:52:05.644][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.647][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.674][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[2023-05-30 01:52:05.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.683][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[2023-05-30 01:52:05.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:05.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:05.808][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-05-30 01:52:05.810][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-05-30 01:52:05.812][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.814][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.815][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.816][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:05.818][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.819][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-05-30 01:52:05.820][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.822][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.823][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-05-30 01:52:05.824][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:05.826][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.827][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-05-30 01:52:05.828][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-05-30 01:52:05.830][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-05-30 01:52:05.831][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:05.833][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:52:05.833][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-05-30 01:52:05.833][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2023-05-30 01:52:05.834][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-05-30 01:52:05.835][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:05.836][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:05.838][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:05.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:05.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:05.841][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:05.843][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-05-30 01:52:05.843][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-05-30 01:52:05.844][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:05.845][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:05.846][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:05.848][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:05.850][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2023-05-30 01:52:05.851][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-30 01:52:05.854][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-30 01:52:05.856][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-30 01:52:05.858][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-30 01:52:05.862][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-05-30 01:52:05.863][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-05-30 01:52:05.865][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-05-30 01:52:05.867][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-05-30 01:52:05.868][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:52:05.870][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:52:05.871][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-05-30 01:52:05.873][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-05-30 01:52:05.874][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-05-30 01:52:05.874][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-05-30 01:52:05.876][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:05.877][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:05.878][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-05-30 01:52:05.879][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-05-30 01:52:05.881][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-05-30 01:52:05.891][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-05-30 01:52:05.892][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:52:05.894][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:52:05.895][private$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[2023-05-30 01:52:05.897][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:52:05.898][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-05-30 01:52:05.900][biodb::testThat]
biodb.INFO [2023-05-30 01:52:05.902][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2023-05-30 01:52:05.903][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:05.904][biodb::testThat]
biodb.DEBUG[2023-05-30 01:52:05.910][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:05.912][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:05.914][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-05-30 01:52:05.916][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:05.917][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-05-30 01:52:05.923][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-05-30 01:52:05.924][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-05-30 01:52:05.926][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-05-30 01:52:05.927][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-05-30 01:52:05.930][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2023-05-30 01:52:05.934][biodb::testThat]
biodb.INFO [2023-05-30 01:52:05.935][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2023-05-30 01:52:05.936][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:05.938][biodb::testThat]
biodb.DEBUG[2023-05-30 01:52:05.941][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-05-30 01:52:05.942][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-05-30 01:52:05.944][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:05.946][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-05-30 01:52:05.949][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-05-30 01:52:05.951][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-30 01:52:05.953][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-05-30 01:52:05.954][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-05-30 01:52:05.977][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-05-30 01:52:05.979][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-05-30 01:52:05.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:52:05.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:05.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:05.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:05.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:05.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:05.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:52:06.000][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.001][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.003][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.004][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.015][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:06.016][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:06.017][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.019][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.020][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:06.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:06.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.030][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:06.031][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:06.033][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.034][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.044][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:06.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:06.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.053][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:06.055][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:06.056][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.058][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.059][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:06.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:06.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.069][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:06.070][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:06.071][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.073][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:06.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:06.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.084][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:06.085][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:06.087][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.088][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:06.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:06.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.099][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:06.100][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:06.102][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.103][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.105][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:06.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:06.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.114][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:06.116][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:06.117][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.118][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.120][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:06.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:06.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.129][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:06.131][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:06.132][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.134][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.135][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:06.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:06.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.145][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:06.146][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:06.148][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.149][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.151][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:06.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:06.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.160][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:06.161][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:06.163][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.164][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.166][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:06.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:06.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.175][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:06.177][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:06.178][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.179][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:06.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:06.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.198][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.200][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.201][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.203][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.205][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.214][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:06.215][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:06.217][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.218][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:06.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:06.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.229][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:06.231][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:06.232][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.234][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:06.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:06.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.244][ef$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:06.246][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:06.247][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.249][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.250][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:06.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:06.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.259][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:06.261][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:06.262][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.264][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.265][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:06.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:06.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.275][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-05-30 01:52:06.276][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:06.277][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.279][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.281][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-05-30 01:52:06.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:06.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.307][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:06.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:06.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.312][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:06.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:06.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.318][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:06.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:06.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.324][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:06.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:06.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.329][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:06.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:06.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.335][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:06.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:06.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:06.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:06.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:06.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:06.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:06.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:06.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:06.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:06.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:06.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:06.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:06.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:06.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.383][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:06.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:06.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.389][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:06.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:06.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.394][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:06.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:06.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.400][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:06.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:06.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.406][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:06.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:06.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.411][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:06.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:06.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.417][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:06.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:06.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.422][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:06.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:06.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.428][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:06.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:06.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.434][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:06.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:06.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.439][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:06.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:06.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.445][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:06.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:06.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.451][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:06.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:06.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.456][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:06.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:06.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.462][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:06.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:06.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:06.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:06.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:06.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:06.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.479][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:06.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:06.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.503][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.509][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:06.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:06.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.514][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:06.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:06.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.520][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:06.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:06.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:06.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:06.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:06.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:06.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:06.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:06.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:06.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:06.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.547][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:06.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:06.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:06.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:06.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.558][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:06.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:06.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.563][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:06.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:06.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.569][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:06.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:06.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.574][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:06.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:06.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.580][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:06.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:06.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.585][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:06.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:06.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.591][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:06.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:06.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:06.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:06.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.602][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:06.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:06.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.607][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-05-30 01:52:06.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.613][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.624][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.637][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-05-30 01:52:06.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:06.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:06.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:06.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:06.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:06.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:06.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:06.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:06.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:06.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.670][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:06.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:06.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.680][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:06.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:06.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.685][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:06.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:06.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.696][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:06.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:06.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:06.739][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-05-30 01:52:06.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:06.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:06.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:06.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:06.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-30 01:52:06.760][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-30 01:52:06.762][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-05-30 01:52:06.764][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-05-30 01:52:06.765][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-30 01:52:06.766][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:06.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:06.769][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:06.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:06.771][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-30 01:52:06.786][biodb::testContext]
biodb.INFO [2023-05-30 01:52:06.793][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:52:06.795][biodb::testContext] Test context - Test search of entries
biodb.INFO [2023-05-30 01:52:06.796][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-30 01:52:06.798][biodb::testContext]
biodb.INFO [2023-05-30 01:52:06.806][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-30 01:52:06.809][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-30 01:52:06.813][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:52:06.815][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-30 01:52:06.816][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-30 01:52:06.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.822][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-30 01:52:06.823][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-30 01:52:06.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.828][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-30 01:52:06.830][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-30 01:52:06.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.833][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[2023-05-30 01:52:06.835][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-30 01:52:06.836][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-30 01:52:06.838][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-30 01:52:06.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.843][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-30 01:52:06.844][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-30 01:52:06.846][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-30 01:52:06.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.851][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-30 01:52:06.852][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-30 01:52:06.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.857][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-30 01:52:06.859][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-30 01:52:06.860][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-30 01:52:06.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.865][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-30 01:52:06.867][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-30 01:52:06.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.872][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-30 01:52:06.873][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-30 01:52:06.875][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-30 01:52:06.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.880][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-30 01:52:06.882][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-30 01:52:06.883][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-30 01:52:06.885][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-30 01:52:06.886][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-30 01:52:06.887][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-30 01:52:06.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.893][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-30 01:52:06.894][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-30 01:52:06.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.899][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-30 01:52:06.901][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-30 01:52:06.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.906][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-30 01:52:06.907][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-30 01:52:06.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.911][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[2023-05-30 01:52:06.912][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-30 01:52:06.914][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-30 01:52:06.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.919][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-30 01:52:06.920][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-30 01:52:06.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.924][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[2023-05-30 01:52:06.926][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-30 01:52:06.927][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-30 01:52:06.931][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-30 01:52:06.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.945][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-30 01:52:06.946][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-30 01:52:06.948][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-30 01:52:06.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:06.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:06.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:06.953][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-30 01:52:06.956][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:06.957][self$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[2023-05-30 01:52:06.959][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:06.960][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:06.962][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:06.963][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:52:06.965][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:06.966][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:06.967][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:52:06.969][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:06.970][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:06.972][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-30 01:52:06.973][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:06.975][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:06.976][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:06.977][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:52:06.977][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:52:06.977][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-30 01:52:06.977][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-30 01:52:06.977][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-30 01:52:06.979][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:52:06.980][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:06.982][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:06.983][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:06.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:06.986][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:06.987][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:06.988][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:06.990][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:06.991][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:06.992][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:06.994][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:06.996][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-30 01:52:06.998][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:06.999][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-30 01:52:07.001][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.002][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:07.004][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.005][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:52:07.006][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:07.008][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:07.009][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-30 01:52:07.011][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:07.012][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.014][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-30 01:52:07.015][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:07.016][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:07.018][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.019][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:52:07.019][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-30 01:52:07.019][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-30 01:52:07.019][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-30 01:52:07.019][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-30 01:52:07.021][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:52:07.022][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:07.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:07.025][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:07.026][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:07.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:07.029][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:07.030][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:07.031][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:07.033][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:07.034][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:07.035][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:07.037][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-30 01:52:07.039][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.041][self$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[2023-05-30 01:52:07.042][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.044][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:07.045][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.046][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:52:07.048][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:07.049][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:07.051][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-30 01:52:07.052][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:07.053][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:07.055][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-30 01:52:07.056][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:07.058][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:07.059][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.061][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:07.062][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:52:07.063][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:07.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:07.066][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:07.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:07.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:07.070][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:07.071][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:07.073][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:07.074][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:07.075][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:07.077][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:07.079][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-30 01:52:07.089][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.090][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-30 01:52:07.092][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.093][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:07.095][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.096][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-30 01:52:07.097][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:07.099][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:07.100][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-30 01:52:07.102][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:07.103][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:07.105][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-30 01:52:07.106][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:07.107][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:07.109][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.110][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:07.112][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-30 01:52:07.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:07.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:07.116][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:07.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:07.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:07.120][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:07.121][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:07.122][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:07.124][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:07.125][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:07.126][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:07.128][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:52:07.130][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.162][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[2023-05-30 01:52:07.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.193][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[2023-05-30 01:52:07.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.199][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[2023-05-30 01:52:07.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.205][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[2023-05-30 01:52:07.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.212][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[2023-05-30 01:52:07.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.218][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[2023-05-30 01:52:07.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.245][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[2023-05-30 01:52:07.246][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-30 01:52:07.248][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-30 01:52:07.250][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-30 01:52:07.252][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-30 01:52:07.254][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-30 01:52:07.256][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-30 01:52:07.258][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-30 01:52:07.260][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-30 01:52:07.262][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-30 01:52:07.264][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-30 01:52:07.270][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-30 01:52:07.273][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-30 01:52:07.275][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-30 01:52:07.277][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-30 01:52:07.280][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-30 01:52:07.282][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-30 01:52:07.284][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-30 01:52:07.287][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-30 01:52:07.289][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-30 01:52:07.291][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-30 01:52:07.293][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-30 01:52:07.296][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-30 01:52:07.298][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-30 01:52:07.300][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-30 01:52:07.302][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-30 01:52:07.305][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-30 01:52:07.307][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-30 01:52:07.309][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-30 01:52:07.312][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-30 01:52:07.314][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-30 01:52:07.316][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-30 01:52:07.319][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-30 01:52:07.321][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-30 01:52:07.324][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-30 01:52:07.326][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-30 01:52:07.328][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-30 01:52:07.330][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-30 01:52:07.333][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-30 01:52:07.335][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-30 01:52:07.337][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-30 01:52:07.339][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-30 01:52:07.342][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-30 01:52:07.344][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-30 01:52:07.346][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-30 01:52:07.348][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-30 01:52:07.351][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-30 01:52:07.353][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-30 01:52:07.355][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-30 01:52:07.358][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-30 01:52:07.360][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-30 01:52:07.362][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-30 01:52:07.364][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-30 01:52:07.366][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-30 01:52:07.368][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-30 01:52:07.371][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-30 01:52:07.374][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-30 01:52:07.376][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-30 01:52:07.379][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-30 01:52:07.438][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-30 01:52:07.441][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-30 01:52:07.443][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-30 01:52:07.445][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-30 01:52:07.447][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-30 01:52:07.449][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-30 01:52:07.452][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-30 01:52:07.453][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-30 01:52:07.456][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-30 01:52:07.458][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-30 01:52:07.460][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-30 01:52:07.462][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-30 01:52:07.464][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-30 01:52:07.466][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-30 01:52:07.468][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-30 01:52:07.470][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-30 01:52:07.472][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-30 01:52:07.474][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-30 01:52:07.476][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-30 01:52:07.478][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-30 01:52:07.480][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-30 01:52:07.482][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-30 01:52:07.484][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-30 01:52:07.485][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-30 01:52:07.487][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-30 01:52:07.489][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-30 01:52:07.492][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-30 01:52:07.493][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-30 01:52:07.494][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.497][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-30 01:52:07.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:07.654][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-05-30 01:52:07.656][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-05-30 01:52:07.658][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:07.660][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-30 01:52:07.661][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.663][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-30 01:52:07.664][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:07.665][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-05-30 01:52:07.667][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.668][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-30 01:52:07.669][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-05-30 01:52:07.671][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-30 01:52:07.672][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.674][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-05-30 01:52:07.675][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-05-30 01:52:07.676][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-05-30 01:52:07.678][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-30 01:52:07.679][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-30 01:52:07.679][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-05-30 01:52:07.679][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2023-05-30 01:52:07.681][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-05-30 01:52:07.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:07.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:07.685][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-30 01:52:07.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-30 01:52:07.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-30 01:52:07.689][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-30 01:52:07.690][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-05-30 01:52:07.690][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-05-30 01:52:07.691][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:07.693][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:07.694][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-30 01:52:07.695][self$setPropertyValue]
biodb.DEBUG[2023-05-30 01:52:07.697][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2023-05-30 01:52:07.699][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-30 01:52:07.701][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-30 01:52:07.703][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-30 01:52:07.706][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-30 01:52:07.710][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-05-30 01:52:07.711][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-05-30 01:52:07.713][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-05-30 01:52:07.715][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-05-30 01:52:07.717][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:52:07.718][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:52:07.720][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-05-30 01:52:07.729][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-05-30 01:52:07.731][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-05-30 01:52:07.731][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-05-30 01:52:07.733][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-30 01:52:07.734][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-30 01:52:07.735][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-05-30 01:52:07.736][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-05-30 01:52:07.738][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-05-30 01:52:07.740][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-05-30 01:52:07.742][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:52:07.743][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:52:07.745][private$addConnectorRules] Create new rule for URL "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-05-30 01:52:07.746][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-30 01:52:07.748][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-05-30 01:52:07.750][biodb::testThat]
biodb.INFO [2023-05-30 01:52:07.751][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2023-05-30 01:52:07.753][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-30 01:52:07.754][biodb::testThat]
biodb.DEBUG[2023-05-30 01:52:07.768][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-05-30 01:52:07.769][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2023-05-30 01:52:07.771][private$doSearchForEntries] fields VALUES = and
biodb.INFO [2023-05-30 01:52:07.775][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2023-05-30 01:52:07.777][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2023-05-30 01:52:07.778][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2023-05-30 01:52:07.780][private$doDownload] Downloading HMDB metabolite database at "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2023-05-30 01:52:07.782][cch$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/R/R-4.3.0/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2023-05-30 01:52:07.784][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2023-05-30 01:52:07.785][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2023-05-30 01:52:07.787][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2023-05-30 01:52:07.789][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2023-05-30 01:52:07.791][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/markerbeae76a5f922emarker".
biodb.TRACE[2023-05-30 01:52:07.793][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2023-05-30 01:52:07.794][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-05-30 01:52:07.796][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2023-05-30 01:52:07.798][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2023-05-30 01:52:07.799][private$doExtractDownload] Extracting content of downloaded',
' HMDB metabolite database...
biodb.DEBUG[2023-05-30 01:52:07.801][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2023-05-30 01:52:07.802][private$doExtractDownload] Unzipping /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /home/biocbuild/.cache/R/biodb/tmp...
biodb.DEBUG[2023-05-30 01:52:07.805][private$findXmlDatabaseFile] Found files [1]: "hmdb_two_full_entries.xml" into /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2023-05-30 01:52:07.806][private$findXmlDatabaseFile] Found XML file /home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2023-05-30 01:52:07.808][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2023-05-30 01:52:07.810][private$doExtractDownload] Extract entries from XML file "/home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2023-05-30 01:52:07.818][self$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[2023-05-30 01:52:07.820][private$doAddFilesToCache] Destination files are [2]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-05-30 01:52:07.821][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-05-30 01:52:07.822][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2023-05-30 01:52:07.825][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/markerbeae77ac2d9a5marker".
biodb.TRACE[2023-05-30 01:52:07.826][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2023-05-30 01:52:07.828][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-05-30 01:52:07.829][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-05-30 01:52:07.831][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:07.832][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-05-30 01:52:07.838][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-05-30 01:52:07.839][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-05-30 01:52:07.841][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-05-30 01:52:07.842][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-05-30 01:52:07.843][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-05-30 01:52:07.845][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2023-05-30 01:52:07.847][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-05-30 01:52:07.849][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-05-30 01:52:07.851][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:07.853][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-05-30 01:52:07.856][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-05-30 01:52:07.857][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-30 01:52:07.860][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-05-30 01:52:07.861][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-05-30 01:52:07.892][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-05-30 01:52:07.894][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-05-30 01:52:07.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:52:07.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:07.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:07.908][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:07.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:07.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:07.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:52:07.917][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:07.918][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:07.920][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:07.921][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:07.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:07.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:07.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:07.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:07.932][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:07.934][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:07.935][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:07.936][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:07.938][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:07.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:07.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:07.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:07.948][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:07.949][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:07.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:07.952][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:07.954][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:07.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:07.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:07.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:07.964][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:07.965][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:07.967][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:07.968][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:07.970][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:07.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:07.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:07.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:07.979][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:07.981][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:07.982][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:07.983][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:07.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:07.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:07.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:07.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:07.995][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:07.996][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:07.998][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:07.999][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:08.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:08.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.010][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.012][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.013][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.014][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.016][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.026][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.027][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.028][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.030][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.032][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.049][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.051][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.052][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.054][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.056][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.065][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.067][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.068][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.070][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.072][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.081][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:08.083][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:08.084][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.086][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.087][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:08.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:08.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.097][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:08.098][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:08.099][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.101][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.103][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:08.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:08.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.112][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.113][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.115][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.116][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.127][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:08.129][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:08.130][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.132][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:08.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:08.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.143][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:08.144][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:08.146][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.147][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:08.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:08.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.158][ef$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:08.159][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:08.161][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.162][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.164][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:08.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:08.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.173][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:08.174][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:08.175][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.177][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.179][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:08.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:08.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.188][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-05-30 01:52:08.189][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:08.191][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.192][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.194][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-05-30 01:52:08.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:08.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:08.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:08.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:08.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:08.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:08.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:08.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.229][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:08.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:08.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.234][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:08.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:08.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.240][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:08.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:08.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.246][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:08.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:08.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.251][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:08.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:08.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.257][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:08.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:08.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:08.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:08.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:08.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:08.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:08.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:08.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:08.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:08.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:08.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:08.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:08.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:08.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.297][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.302][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.308][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.314][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.319][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.325][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.331][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:08.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:08.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.337][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:08.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:08.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.342][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:08.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:08.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.357][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:08.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:08.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.363][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:08.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:08.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.369][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:08.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:08.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.374][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:08.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:08.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.380][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:08.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:08.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.386][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:08.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:08.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:08.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:08.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:08.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:08.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.403][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:08.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:08.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.415][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.426][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.432][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.438][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:08.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:08.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:08.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:08.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:08.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:08.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:08.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:08.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:08.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:08.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:08.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:08.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.479][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.485][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.491][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.497][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:08.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:08.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.511][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:08.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:08.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.517][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:08.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:08.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.523][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:08.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:08.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.529][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:08.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:08.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.535][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:08.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:08.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.541][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-05-30 01:52:08.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.565][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-05-30 01:52:08.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.575][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:08.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:08.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:08.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:08.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:08.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:08.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:08.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:08.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:08.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:08.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.608][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:08.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:08.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.614][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:08.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:08.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:08.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:08.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.625][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:08.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:08.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:08.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:08.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:08.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:08.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:08.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:08.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:08.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:08.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:08.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:08.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:08.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:08.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:08.677][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-05-30 01:52:08.678][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:08.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:08.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.684][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:08.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:08.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.689][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:08.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:08.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.695][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:08.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:08.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:08.700][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-05-30 01:52:08.702][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-05-30 01:52:08.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:52:08.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:08.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:08.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:08.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:08.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:08.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:08.719][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-05-30 01:52:08.720][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-05-30 01:52:08.723][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:08.724][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-05-30 01:52:08.727][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-05-30 01:52:08.729][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-30 01:52:08.731][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-05-30 01:52:08.732][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-05-30 01:52:08.755][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-05-30 01:52:08.757][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-05-30 01:52:08.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:52:08.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:08.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:08.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:08.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:08.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:08.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:52:08.777][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:08.779][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:08.780][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.782][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:08.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:08.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.792][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:08.794][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:08.795][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.796][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.798][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:08.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:08.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.816][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:08.818][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:08.819][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.820][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.822][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:08.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:08.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.831][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:08.833][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:08.834][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.836][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.838][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:08.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:08.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.847][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:08.849][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:08.850][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.851][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:08.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:08.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.862][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:08.864][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:08.865][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.867][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:08.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:08.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.878][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.879][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.881][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.882][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.884][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:08.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.893][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.895][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.896][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.897][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.899][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:08.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.908][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.910][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.911][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.912][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.914][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:08.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.923][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.925][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.926][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.927][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.929][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:08.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.939][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:08.940][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:08.942][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.943][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.945][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:08.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:08.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.962][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:08.964][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:08.965][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.967][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.968][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:08.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:08.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.978][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.979][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.981][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.982][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.984][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:08.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.993][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:08.995][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:08.996][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:08.998][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:08.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:09.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:09.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.009][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:09.011][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:09.012][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.013][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:09.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:09.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.024][ef$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.025][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.026][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.028][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.029][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.038][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:09.040][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:09.041][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.042][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.044][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:09.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:09.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.053][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-05-30 01:52:09.055][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:09.056][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.057][ef$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.059][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-05-30 01:52:09.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:09.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:09.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:09.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:09.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:09.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:09.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:09.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.085][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:09.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:09.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.090][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:09.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:09.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.096][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-30 01:52:09.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-30 01:52:09.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.101][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:09.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:09.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.115][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:09.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:09.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.121][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-05-30 01:52:09.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-05-30 01:52:09.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:09.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:09.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:09.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:09.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-30 01:52:09.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-30 01:52:09.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:09.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:09.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:09.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:09.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:09.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-05-30 01:52:09.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.160][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:09.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:09.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.166][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:09.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:09.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.171][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:09.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-30 01:52:09.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.177][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:09.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:09.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.182][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:09.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:09.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.188][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:09.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-05-30 01:52:09.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.194][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:09.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:09.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.199][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:09.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:09.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.205][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:09.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-05-30 01:52:09.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.210][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.216][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.222][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.227][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:09.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:09.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.233][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:09.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:09.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.238][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-30 01:52:09.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-30 01:52:09.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.244][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:09.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:09.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:09.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:09.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-30 01:52:09.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-30 01:52:09.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.275][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.280][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.286][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:09.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:09.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.292][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:09.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:09.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.297][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:09.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-30 01:52:09.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:09.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:09.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:09.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:09.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:09.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-30 01:52:09.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.320][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:09.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:09.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:09.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:09.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.331][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:09.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:09.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.336][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:09.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:09.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.342][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:09.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:09.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.347][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:09.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-30 01:52:09.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.353][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:09.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:09.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.358][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:09.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:09.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.364][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:09.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-05-30 01:52:09.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.369][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:09.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:09.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.375][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:09.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:09.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.380][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-30 01:52:09.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-30 01:52:09.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.386][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-05-30 01:52:09.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.417][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-05-30 01:52:09.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-30 01:52:09.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:09.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:09.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:09.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:09.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:09.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:09.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.444][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:09.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:09.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.450][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-30 01:52:09.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-30 01:52:09.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.459][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:09.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:09.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.465][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:09.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:09.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:09.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:09.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.481][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:09.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-30 01:52:09.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:09.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:09.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:09.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:09.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:09.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:09.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:09.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:09.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:09.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:09.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-30 01:52:09.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-30 01:52:09.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:09.530][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-05-30 01:52:09.531][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.537][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.544][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.550][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:09.572][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-05-30 01:52:09.573][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2023-05-30 01:52:09.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:52:09.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:09.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:09.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:09.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:09.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:09.591][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[2023-05-30 01:52:09.607][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-05-30 01:52:09.609][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-05-30 01:52:09.610][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-05-30 01:52:09.613][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:09.615][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:09.617][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-05-30 01:52:09.619][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:09.620][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-05-30 01:52:09.626][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-05-30 01:52:09.627][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-05-30 01:52:09.629][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-05-30 01:52:09.630][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-05-30 01:52:09.631][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-05-30 01:52:09.633][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-05-30 01:52:09.635][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.641][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.647][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.652][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.658][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.663][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.668][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:09.674][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-05-30 01:52:09.675][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-05-30 01:52:09.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:52:09.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:09.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:09.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:09.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:09.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:09.691][FUN] Functions in observer BiodbConfig: [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[2023-05-30 01:52:09.692][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.698][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.704][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.709][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.723][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.729][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.734][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:09.739][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-05-30 01:52:09.741][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-05-30 01:52:09.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:52:09.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:09.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:09.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:09.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:09.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:09.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-30 01:52:09.771][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-05-30 01:52:09.772][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-05-30 01:52:09.774][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-05-30 01:52:09.776][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:09.778][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:09.780][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-05-30 01:52:09.781][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-05-30 01:52:09.783][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-05-30 01:52:09.788][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-05-30 01:52:09.789][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-05-30 01:52:09.791][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-05-30 01:52:09.792][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-05-30 01:52:09.793][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-05-30 01:52:09.795][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-05-30 01:52:09.797][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.803][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.808][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.813][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.819][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.824][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.830][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:09.835][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-05-30 01:52:09.837][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2023-05-30 01:52:09.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:52:09.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:09.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:09.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:09.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:09.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:09.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-30 01:52:09.853][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.867][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.873][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.879][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.884][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.890][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-30 01:52:09.896][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-05-30 01:52:09.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-05-30 01:52:09.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-30 01:52:09.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-30 01:52:09.901][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-05-30 01:52:09.902][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-05-30 01:52:09.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-30 01:52:09.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:09.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:09.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:09.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:09.917][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:09.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-30 01:52:09.922][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-30 01:52:09.924][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-05-30 01:52:09.926][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-05-30 01:52:09.927][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-30 01:52:09.928][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-30 01:52:09.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-30 01:52:09.931][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-30 01:52:09.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-30 01:52:09.933][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-30 01:52:09.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 199 ]
>
> proc.time()
user system elapsed
13.181 0.612 19.809
biodbHmdb.Rcheck/biodbHmdb-Ex.timings
| name | user | system | elapsed | |
| HmdbMetabolitesConn | 0.651 | 0.024 | 0.674 | |
| HmdbMetabolitesEntry | 0.214 | 0.001 | 0.216 | |