Pierrick Roger
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/biodbHmdb |
| git_branch: RELEASE_3_16 |
| git_last_commit: df94f3a |
| git_last_commit_date: 2022-11-01 11:26:07 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:04:59 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 182/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbHmdb 1.4.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: biodbHmdb |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings biodbHmdb_1.4.0.tar.gz |
| StartedAt: 2023-04-10 19:18:44 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 19:19:48 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 63.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbHmdb.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings biodbHmdb_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/biodbHmdb.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.4.0’
* 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
* checking installed package size ... NOTE
installed size is 9.8Mb
sub-directories of 1Mb or more:
libs 9.2Mb
* 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-3.16-bioc/meat/biodbHmdb.Rcheck/00check.log’
for details.
biodbHmdb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL biodbHmdb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘biodbHmdb’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c Tag.cpp -o Tag.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractXmlEntries.cpp -o extractXmlEntries.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-100-tag.cpp -o test-100-tag.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so RcppExports.o Tag.o extractXmlEntries.o test-100-tag.o test-runner.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-biodbHmdb/00new/biodbHmdb/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbHmdb)
biodbHmdb.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 [2023-04-10 19:19:30.345][biodb::testContext]
biodb.INFO [2023-04-10 19:19:30.348][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:19:30.349][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2023-04-10 19:19:30.350][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:19:30.351][biodb::testContext]
biodb.INFO [2023-04-10 19:19:30.353][biodb::testThat]
biodb.INFO [2023-04-10 19:19:30.354][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2023-04-10 19:19:30.355][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:30.356][biodb::testThat]
biodb.INFO [2023-04-10 19:19:30.448][biodb::testContext]
biodb.INFO [2023-04-10 19:19:30.449][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:19:30.450][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-04-10 19:19:30.451][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:19:30.452][biodb::testContext]
biodb.INFO [2023-04-10 19:19:30.461][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:19:30.463][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-10 19:19:30.470][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:30.471][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-10 19:19:30.473][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-10 19:19:30.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.476][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-10 19:19:30.501][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-10 19:19:30.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.504][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-10 19:19:30.505][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-10 19:19:30.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.509][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-10 19:19:30.510][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-10 19:19:30.511][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-10 19:19:30.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.514][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-10 19:19:30.515][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-10 19:19:30.517][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-10 19:19:30.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.520][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-10 19:19:30.521][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-10 19:19:30.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.525][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-10 19:19:30.525][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-10 19:19:30.526][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-10 19:19:30.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.530][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-10 19:19:30.531][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-10 19:19:30.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.534][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-10 19:19:30.535][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-10 19:19:30.536][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-10 19:19:30.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.540][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:19:30.541][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-10 19:19:30.541][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-10 19:19:30.542][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-10 19:19:30.543][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-10 19:19:30.544][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-10 19:19:30.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.548][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-10 19:19:30.549][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-10 19:19:30.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.553][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-10 19:19:30.554][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-10 19:19:30.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.556][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[2023-04-10 19:19:30.557][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-10 19:19:30.558][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-10 19:19:30.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.562][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-10 19:19:30.563][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-10 19:19:30.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.567][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-10 19:19:30.568][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-10 19:19:30.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.571][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:19:30.572][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-10 19:19:30.577][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-10 19:19:30.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.581][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-10 19:19:30.582][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-10 19:19:30.583][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-10 19:19:30.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.589][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-10 19:19:30.623][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:30.638][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-10 19:19:30.639][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.640][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:30.641][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.642][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:30.643][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:30.644][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:30.645][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:19:30.646][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:30.647][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.653][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-10 19:19:30.654][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:30.655][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.656][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.657][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:30.657][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:19:30.657][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:19:30.657][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:19:30.657][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:19:30.658][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:30.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:30.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:30.661][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:30.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:30.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:30.663][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:30.664][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.665][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:30.666][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:30.667][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:30.667][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.669][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-10 19:19:30.670][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:30.671][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:19:30.672][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.673][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:30.674][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.675][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:30.676][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:30.677][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:30.678][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:19:30.679][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:30.680][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.680][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-10 19:19:30.681][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:30.682][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.683][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.684][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:30.684][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:19:30.684][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:19:30.684][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:19:30.684][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:19:30.685][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:30.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:30.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:30.688][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:30.689][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:30.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:30.691][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:30.692][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.693][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:30.694][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:30.695][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:30.696][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.697][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-10 19:19:30.698][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.700][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-10 19:19:30.700][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.701][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:30.702][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.703][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:30.704][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:30.705][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:30.706][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:19:30.707][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:30.708][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:30.709][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-10 19:19:30.710][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:30.711][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.712][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.713][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.714][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:30.715][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:30.716][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:30.717][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:30.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:30.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:30.719][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:30.720][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.721][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:30.722][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:30.723][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:30.724][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.725][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-10 19:19:30.727][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.728][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:19:30.729][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.730][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:30.731][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.732][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:30.733][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:30.734][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:30.735][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:19:30.736][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:30.737][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:30.737][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-10 19:19:30.738][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:30.739][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.740][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:30.741][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.742][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:30.743][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:30.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:30.745][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:30.746][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:30.747][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:30.748][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:30.749][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.750][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:30.750][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:30.751][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:30.752][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:30.756][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:30.757][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.789][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[2023-04-10 19:19:30.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:30.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:30.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:30.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:30.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:30.837][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-10 19:19:30.842][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-10 19:19:30.844][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-10 19:19:30.845][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-10 19:19:30.846][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:19:30.848][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:19:30.849][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-10 19:19:30.850][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-10 19:19:30.851][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-10 19:19:30.853][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:19:30.854][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:19:30.855][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-10 19:19:30.857][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-10 19:19:30.858][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-10 19:19:30.859][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-10 19:19:30.861][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:19:30.862][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-10 19:19:30.863][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-10 19:19:30.865][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:19:30.866][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-10 19:19:30.868][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-10 19:19:30.869][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-10 19:19:30.870][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-10 19:19:30.872][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-10 19:19:30.873][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-10 19:19:30.874][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-10 19:19:30.876][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-10 19:19:30.877][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-10 19:19:30.878][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-10 19:19:30.880][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-10 19:19:30.881][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-10 19:19:30.882][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-10 19:19:30.883][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-10 19:19:30.885][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-10 19:19:30.886][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-10 19:19:30.887][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-10 19:19:30.889][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-10 19:19:30.890][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-10 19:19:30.891][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-10 19:19:30.893][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-10 19:19:30.894][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-10 19:19:30.895][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-10 19:19:30.897][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-10 19:19:30.898][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-10 19:19:30.899][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-10 19:19:30.901][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-10 19:19:30.902][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-10 19:19:30.903][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-10 19:19:30.905][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-10 19:19:30.906][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-10 19:19:30.907][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-10 19:19:30.908][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-10 19:19:30.910][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-10 19:19:30.911][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-10 19:19:30.912][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-10 19:19:30.914][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-10 19:19:30.915][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-10 19:19:30.916][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-10 19:19:30.918][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-10 19:19:30.919][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-10 19:19:30.920][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-10 19:19:30.921][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-10 19:19:30.923][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-10 19:19:30.924][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-10 19:19:30.926][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-10 19:19:30.927][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-10 19:19:30.928][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:19:30.929][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:19:30.931][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-10 19:19:30.932][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-10 19:19:30.933][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-10 19:19:30.935][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-10 19:19:30.936][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-10 19:19:30.937][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-10 19:19:30.939][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-10 19:19:30.940][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-10 19:19:30.941][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-10 19:19:30.942][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-10 19:19:30.944][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-10 19:19:30.945][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-10 19:19:30.946][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-10 19:19:30.948][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-10 19:19:30.986][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-10 19:19:30.992][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-10 19:19:30.994][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:19:30.998][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:30.999][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.000][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.017][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[2023-04-10 19:19:31.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.023][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[2023-04-10 19:19:31.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.029][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[2023-04-10 19:19:31.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.066][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[2023-04-10 19:19:31.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.073][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[2023-04-10 19:19:31.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.085][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[2023-04-10 19:19:31.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.110][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-04-10 19:19:31.120][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-04-10 19:19:31.122][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.123][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.124][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.125][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:31.126][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.127][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-04-10 19:19:31.128][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.129][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.130][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-10 19:19:31.136][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:31.137][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.137][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-04-10 19:19:31.138][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-04-10 19:19:31.139][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-04-10 19:19:31.140][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.141][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:31.141][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-04-10 19:19:31.142][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-10 19:19:31.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:31.144][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:31.145][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:31.146][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:31.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:31.147][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.148][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-10 19:19:31.148][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-04-10 19:19:31.149][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:31.150][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:31.151][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.152][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.158][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:19:31.159][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:19:31.161][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:19:31.162][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:19:31.189][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-04-10 19:19:31.190][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-04-10 19:19:31.195][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-10 19:19:31.199][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-10 19:19:31.203][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:31.204][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:31.206][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-04-10 19:19:31.207][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-04-10 19:19:31.208][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-10 19:19:31.208][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-04-10 19:19:31.209][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:31.210][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:31.210][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-04-10 19:19:31.211][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-04-10 19:19:31.212][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-10 19:19:31.228][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-10 19:19:31.230][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:31.231][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:31.232][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-10 19:19:31.233][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:31.234][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-04-10 19:19:31.242][biodb::testThat]
biodb.INFO [2023-04-10 19:19:31.243][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-04-10 19:19:31.244][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:31.245][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:31.250][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2023-04-10 19:19:31.251][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:31.255][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-10 19:19:31.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:31.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:31.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:31.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.274][FUN] Functions in observer BiodbConfig: [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[2023-04-10 19:19:31.287][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.288][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.289][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.290][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.320][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:31.321][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:31.321][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.322][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.347][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:31.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:31.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.351][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:31.352][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:31.353][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.354][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.355][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:31.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:31.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.359][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:31.360][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:31.361][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.362][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:31.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:31.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.368][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.369][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.369][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.370][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.376][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:31.377][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:31.378][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.378][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.380][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:31.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:31.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.384][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.385][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.386][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.387][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.388][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.392][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:31.393][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:31.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.395][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.396][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:31.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:31.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.400][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:31.401][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:31.402][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.403][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.404][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:31.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:31.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.408][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:31.409][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:31.410][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.411][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.412][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:31.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:31.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.416][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:31.417][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:31.418][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.418][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:31.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:31.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.424][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.425][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.425][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.426][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.432][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.436][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:31.437][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:31.438][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.439][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:31.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:31.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.444][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:31.445][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:31.446][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.447][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:31.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:31.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.452][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:31.453][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:31.453][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.454][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.456][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:31.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:31.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.459][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:31.460][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:31.461][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.462][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.464][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:31.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:31.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.467][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-10 19:19:31.468][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:31.469][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.470][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.472][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-10 19:19:31.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:31.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.517][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:31.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:31.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.521][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:31.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:31.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.525][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:31.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:31.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.528][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:31.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:31.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.532][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:31.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:31.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.536][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:31.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:31.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:31.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:31.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:31.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:31.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:31.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:31.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.566][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:31.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:31.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.570][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:31.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:31.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.573][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:31.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:31.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.577][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:31.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:31.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.581][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:31.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:31.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.585][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:31.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:31.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.589][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:31.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:31.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.592][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:31.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:31.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.596][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:31.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:31.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.600][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:31.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:31.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.603][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:31.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:31.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.607][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:31.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:31.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.611][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:31.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:31.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.614][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:31.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:31.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.618][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:31.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:31.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:31.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:31.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:31.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:31.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.629][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:31.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:31.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.645][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:31.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:31.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.649][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:31.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:31.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.653][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:31.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:31.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:31.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:31.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:31.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:31.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:31.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:31.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:31.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:31.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:31.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:31.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:31.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:31.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.684][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.688][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.692][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.695][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:31.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:31.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.699][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:31.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:31.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.703][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:31.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:31.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.707][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-10 19:19:31.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.711][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.715][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.719][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.723][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-10 19:19:31.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:31.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.745][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:31.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:31.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.749][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:31.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:31.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.753][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:31.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:31.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.757][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:31.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:31.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:31.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:31.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.765][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.769][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.782][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:31.808][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2023-04-10 19:19:31.811][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:31.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:31.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.815][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:31.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:31.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.818][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:31.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:31.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.822][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:31.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:31.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.851][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.885][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.889][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.893][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:31.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.926][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.928][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.928][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.929][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:31.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:31.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.956][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.957][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.958][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.959][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:31.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.973][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.978][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.982][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.986][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.987][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.988][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.989][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:31.990][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:31.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:31.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.015][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.017][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.018][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.019][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.032][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.036][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.040][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.051][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.052][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.053][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.054][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.055][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.065][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.069][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.077][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.078][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.079][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.080][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.081][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.093][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:32.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:32.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.097][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:32.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:32.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.101][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:32.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:32.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.106][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:32.107][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:32.108][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.109][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.110][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:32.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:32.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.121][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.125][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.129][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.133][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.134][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.135][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.136][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.137][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.148][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.152][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.156][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.160][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.161][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.162][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.163][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.164][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.192][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.193][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.194][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.194][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.206][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.210][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.214][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.218][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.219][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.220][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.221][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.222][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.233][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.238][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.242][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.246][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.247][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.248][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.249][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.250][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.261][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.265][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.269][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.273][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.274][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.275][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.276][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.277][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.288][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:32.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:32.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.293][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:32.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:32.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.303][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:32.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:32.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.307][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:32.308][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:32.309][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.310][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.311][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:32.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:32.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.321][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:32.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:32.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:32.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:32.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:32.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:32.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.333][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:32.335][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:32.336][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.336][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:32.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:32.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.353][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.360][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.362][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.362][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.363][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.375][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.379][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.383][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.387][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.388][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.390][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.391][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.402][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.403][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.404][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.405][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.410][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.411][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.412][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.413][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.423][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.424][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.425][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.426][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.431][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.432][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.433][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.434][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.439][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:32.440][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:32.441][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.442][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.447][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.448][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.449][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.449][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.455][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.456][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.457][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.458][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.463][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.464][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.465][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.466][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.471][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:32.473][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:32.473][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.474][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.480][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.481][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.482][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.483][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.488][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:32.489][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:32.490][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.491][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.496][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.498][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.499][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.500][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.505][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.506][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.507][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.508][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.513][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.514][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.515][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.515][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.521][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.522][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.523][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.524][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.529][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.530][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.531][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.532][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.542][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:32.544][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:32.545][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.545][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:32.552][biodb::testThat]
biodb.INFO [2023-04-10 19:19:32.553][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-10 19:19:32.554][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:32.555][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:32.568][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-04-10 19:19:32.576][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-10 19:19:32.580][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:32.581][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-10 19:19:32.584][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-04-10 19:19:32.585][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:32.587][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-04-10 19:19:32.589][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:32.612][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:32.613][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-10 19:19:32.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:32.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:32.629][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.630][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.631][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.632][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.638][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.639][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.640][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.641][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.642][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.646][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.647][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.648][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.649][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.650][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.654][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.662][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.663][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.664][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.670][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:32.671][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:32.672][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.673][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:32.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:32.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.678][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.679][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.680][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.681][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.683][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.687][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.688][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.689][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.689][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.691][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.695][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.696][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.697][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.698][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.699][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.703][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.704][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.705][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.706][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.707][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.711][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.712][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.713][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.714][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.715][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.719][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:32.720][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:32.721][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.722][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:32.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:32.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.728][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.729][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.730][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.731][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.736][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.737][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.738][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.739][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.744][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.745][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.746][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.747][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.748][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.752][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:32.753][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:32.754][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.755][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.756][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:32.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:32.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.760][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:32.761][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:32.762][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.763][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.765][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:32.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:32.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.769][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-10 19:19:32.770][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.771][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.772][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.773][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-10 19:19:32.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.795][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.799][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.803][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:32.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.807][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.810][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.814][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:32.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:32.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:32.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:32.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:32.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:32.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:32.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.842][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.846][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.850][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.854][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.858][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.862][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:32.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.866][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.870][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.874][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:32.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.878][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:32.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:32.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.882][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:32.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:32.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.886][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:32.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:32.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.890][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.894][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.903][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.907][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:32.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:32.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.911][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:32.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:32.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:32.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:32.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.931][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.935][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.939][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.966][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.970][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.974][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.978][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:32.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:32.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.982][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:32.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:32.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.986][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:32.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:32.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.990][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-10 19:19:32.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.994][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.998][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:32.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:33.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.002][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:33.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:33.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.006][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-10 19:19:33.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:33.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.024][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.036][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:33.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:33.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.040][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:33.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:33.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.048][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:33.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:33.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.076][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-04-10 19:19:33.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-10 19:19:33.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-10 19:19:33.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-10 19:19:33.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-10 19:19:33.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-10 19:19:33.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-10 19:19:33.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:33.095][biodb::testThat]
biodb.INFO [2023-04-10 19:19:33.097][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-10 19:19:33.098][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:33.099][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:33.102][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.103][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.104][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.105][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.106][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2023-04-10 19:19:33.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.155][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2023-04-10 19:19:33.157][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-04-10 19:19:33.157][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-04-10 19:19:33.158][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-04-10 19:19:33.160][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:33.162][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:33.163][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-10 19:19:33.164][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:33.165][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-10 19:19:33.167][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-10 19:19:33.168][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-10 19:19:33.169][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-10 19:19:33.170][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-10 19:19:33.171][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-10 19:19:33.172][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-10 19:19:33.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.178][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.182][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.186][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.190][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-10 19:19:33.191][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-10 19:19:33.192][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2023-04-10 19:19:33.206][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:33.207][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:33.208][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.209][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.211][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2023-04-10 19:19:33.224][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:33.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:33.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.228][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:33.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:33.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.232][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:33.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:33.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.238][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[2023-04-10 19:19:33.292][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-04-10 19:19:33.293][private$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[2023-04-10 19:19:33.294][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2023-04-10 19:19:33.308][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:33.310][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:33.311][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-10 19:19:33.313][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:33.314][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-10 19:19:33.328][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-10 19:19:33.329][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-10 19:19:33.330][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-10 19:19:33.331][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-10 19:19:33.332][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-10 19:19:33.333][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-10 19:19:33.335][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:33.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:33.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.343][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:33.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:33.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.347][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:33.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:33.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.350][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:33.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:33.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.354][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-10 19:19:33.355][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-10 19:19:33.356][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2023-04-10 19:19:33.370][biodb::testThat]
biodb.INFO [2023-04-10 19:19:33.371][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-04-10 19:19:33.373][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:33.373][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:33.388][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.432][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-04-10 19:19:33.434][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-04-10 19:19:33.436][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-04-10 19:19:33.439][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:33.441][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:33.443][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-10 19:19:33.446][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:33.447][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-10 19:19:33.449][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-10 19:19:33.451][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-10 19:19:33.452][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-10 19:19:33.454][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-10 19:19:33.455][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-10 19:19:33.457][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-10 19:19:33.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.478][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.484][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-10 19:19:33.486][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2023-04-10 19:19:33.518][biodb::testThat]
biodb.INFO [2023-04-10 19:19:33.519][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-04-10 19:19:33.520][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:33.521][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:33.542][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:33.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:33.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.547][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:33.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:33.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.552][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:33.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:33.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.556][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:33.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:33.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.603][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:33.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:33.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.608][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:33.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:33.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.612][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:33.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:33.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.652][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:33.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:33.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:33.661][biodb::testThat]
biodb.INFO [2023-04-10 19:19:33.662][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-10 19:19:33.663][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:33.664][biodb::testThat]
biodb.INFO [2023-04-10 19:19:33.669][biodb::testThat]
biodb.INFO [2023-04-10 19:19:33.670][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-10 19:19:33.671][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:33.672][biodb::testThat]
biodb.INFO [2023-04-10 19:19:33.677][biodb::testThat]
biodb.INFO [2023-04-10 19:19:33.678][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-10 19:19:33.679][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:33.680][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:33.684][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2023-04-10 19:19:34.860][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2023-04-10 19:19:34.899][biodb::testThat]
biodb.INFO [2023-04-10 19:19:34.901][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-10 19:19:34.902][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:34.904][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:35.219][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2023-04-10 19:19:35.237][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:35.239][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:35.241][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.242][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.244][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:35.245][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:35.247][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.248][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:35.249][biodb::testThat]
biodb.INFO [2023-04-10 19:19:35.250][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-04-10 19:19:35.251][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:35.252][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:35.254][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-04-10 19:19:35.309][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-10 19:19:35.311][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:35.313][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-10 19:19:35.329][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-04-10 19:19:35.331][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:35.332][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:35.333][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:35.335][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:35.336][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:35.337][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-10 19:19:35.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:35.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:35.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:35.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.350][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.TRACE[2023-04-10 19:19:35.352][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:35.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:35.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.356][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:35.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:35.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:35.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:35.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:35.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:35.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:35.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:35.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:35.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:35.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:35.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:35.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:35.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:35.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:35.392][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-04-10 19:19:35.393][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-04-10 19:19:35.410][biodb::testThat]
biodb.INFO [2023-04-10 19:19:35.411][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-04-10 19:19:35.412][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:35.413][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:35.421][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2023-04-10 19:19:35.422][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2023-04-10 19:19:35.423][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-10 19:19:35.425][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:35.427][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-10 19:19:35.429][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2023-04-10 19:19:35.430][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:19:35.432][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:19:35.433][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:35.434][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:35.435][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:35.437][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-10 19:19:35.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:35.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:35.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:35.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:35.450][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:35.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:35.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.455][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:35.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:35.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:35.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:35.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:35.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:35.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:35.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:35.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:35.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:35.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:35.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:35.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:35.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:35.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:35.494][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-04-10 19:19:35.501][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-04-10 19:19:35.503][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2023-04-10 19:19:35.521][biodb::testThat]
biodb.INFO [2023-04-10 19:19:35.522][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-04-10 19:19:35.524][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:35.525][biodb::testThat]
biodb.INFO [2023-04-10 19:19:35.548][biodb::testThat]
biodb.INFO [2023-04-10 19:19:35.549][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-04-10 19:19:35.551][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:35.552][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:35.555][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:35.557][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:35.558][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-10 19:19:35.560][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:35.561][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-10 19:19:35.562][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-10 19:19:35.563][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-10 19:19:35.564][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-10 19:19:35.565][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2023-04-10 19:19:35.572][biodb::testThat]
biodb.INFO [2023-04-10 19:19:35.573][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-04-10 19:19:35.575][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:35.576][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:35.578][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:35.580][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:35.594][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-10 19:19:35.597][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:35.598][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-10 19:19:35.600][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-10 19:19:35.601][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-10 19:19:35.602][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-10 19:19:35.603][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2023-04-10 19:19:35.610][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:35.611][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:35.612][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.613][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.614][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:35.616][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:35.617][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.618][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:35.619][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-10 19:19:35.620][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-04-10 19:19:35.628][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-04-10 19:19:35.629][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-10 19:19:35.630][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:35.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:35.632][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.633][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.634][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.INFO [2023-04-10 19:19:35.638][biodb::testContext]
biodb.INFO [2023-04-10 19:19:35.639][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:19:35.640][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2023-04-10 19:19:35.641][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:19:35.642][biodb::testContext]
biodb.INFO [2023-04-10 19:19:35.646][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:19:35.647][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-10 19:19:35.651][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:35.652][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-10 19:19:35.653][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-10 19:19:35.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.657][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-10 19:19:35.658][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-10 19:19:35.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.661][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-10 19:19:35.663][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-10 19:19:35.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.666][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-10 19:19:35.667][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-10 19:19:35.668][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-10 19:19:35.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.672][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-10 19:19:35.673][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-10 19:19:35.674][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-10 19:19:35.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.677][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-10 19:19:35.678][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-10 19:19:35.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.682][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-10 19:19:35.683][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-10 19:19:35.684][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-10 19:19:35.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.694][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-10 19:19:35.695][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-10 19:19:35.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.698][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-10 19:19:35.699][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-10 19:19:35.700][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-10 19:19:35.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.704][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:19:35.704][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-10 19:19:35.705][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-10 19:19:35.706][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-10 19:19:35.707][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-10 19:19:35.708][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-10 19:19:35.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.712][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-10 19:19:35.713][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-10 19:19:35.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.716][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-10 19:19:35.717][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-10 19:19:35.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.720][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[2023-04-10 19:19:35.721][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-10 19:19:35.722][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-10 19:19:35.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.725][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-10 19:19:35.726][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-10 19:19:35.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.729][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[2023-04-10 19:19:35.730][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-10 19:19:35.731][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-10 19:19:35.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.735][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:19:35.736][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-10 19:19:35.741][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-10 19:19:35.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.745][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-10 19:19:35.746][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-10 19:19:35.747][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-10 19:19:35.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.751][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-10 19:19:35.753][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:35.754][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-10 19:19:35.755][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.756][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:35.757][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.758][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:35.758][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:35.759][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:35.760][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:19:35.761][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:35.762][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.763][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-10 19:19:35.764][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:35.765][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.766][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.767][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:35.767][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:19:35.767][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:19:35.767][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:19:35.767][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:19:35.768][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:35.769][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:35.770][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:35.771][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:35.772][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:35.773][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:35.773][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:35.774][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.775][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:35.781][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:35.783][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:35.784][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.785][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-10 19:19:35.787][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:35.788][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:19:35.789][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.789][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:35.790][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.791][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:35.792][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:35.793][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:35.794][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:19:35.795][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:35.796][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.797][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-10 19:19:35.798][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:35.799][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.800][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.801][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:35.801][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:19:35.801][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:19:35.801][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:19:35.801][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:19:35.802][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:35.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:35.803][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:35.804][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:35.805][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:35.806][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:35.807][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:35.808][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.809][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:35.810][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:35.811][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:35.812][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.813][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-10 19:19:35.815][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.816][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-10 19:19:35.816][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.817][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:35.818][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.819][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:35.820][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:35.821][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:35.822][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:19:35.823][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:35.824][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:35.825][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-10 19:19:35.826][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:35.827][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.828][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.829][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.830][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:35.831][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:35.832][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:35.833][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:35.834][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:35.835][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:35.836][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:35.837][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.838][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:35.838][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:35.839][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:35.840][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.842][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-10 19:19:35.843][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.844][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:19:35.845][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.846][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:35.847][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.848][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:35.849][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:35.850][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:35.851][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:19:35.852][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:35.853][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:35.854][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-10 19:19:35.855][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:35.856][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.857][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:35.858][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.859][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:35.860][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:35.861][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:35.862][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:35.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:35.869][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:35.871][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:35.872][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.873][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:35.874][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:35.874][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:35.875][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:35.877][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:35.878][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.883][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[2023-04-10 19:19:35.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.891][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[2023-04-10 19:19:35.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.904][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[2023-04-10 19:19:35.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.918][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[2023-04-10 19:19:35.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:35.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:35.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:35.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:35.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:35.959][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-10 19:19:35.960][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-10 19:19:35.962][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-10 19:19:35.963][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-10 19:19:35.964][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:19:35.966][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:19:35.967][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-10 19:19:35.968][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-10 19:19:35.970][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-10 19:19:35.971][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:19:35.972][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:19:35.974][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-10 19:19:35.975][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-10 19:19:35.976][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-10 19:19:35.978][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-10 19:19:35.979][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:19:35.980][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-10 19:19:35.982][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-10 19:19:35.983][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:19:35.984][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-10 19:19:35.986][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-10 19:19:35.987][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-10 19:19:35.989][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-10 19:19:35.990][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-10 19:19:35.991][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-10 19:19:35.993][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-10 19:19:35.994][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-10 19:19:35.995][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-10 19:19:35.997][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-10 19:19:35.998][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-10 19:19:36.000][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-10 19:19:36.001][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-10 19:19:36.002][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-10 19:19:36.004][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-10 19:19:36.005][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-10 19:19:36.006][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-10 19:19:36.008][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-10 19:19:36.009][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-10 19:19:36.011][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-10 19:19:36.012][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-10 19:19:36.013][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-10 19:19:36.015][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-10 19:19:36.016][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-10 19:19:36.017][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-10 19:19:36.019][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-10 19:19:36.020][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-10 19:19:36.022][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-10 19:19:36.023][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-10 19:19:36.024][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-10 19:19:36.026][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-10 19:19:36.027][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-10 19:19:36.029][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-10 19:19:36.030][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-10 19:19:36.032][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-10 19:19:36.033][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-10 19:19:36.042][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-10 19:19:36.044][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-10 19:19:36.046][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-10 19:19:36.047][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-10 19:19:36.049][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-10 19:19:36.050][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-10 19:19:36.051][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-10 19:19:36.053][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-10 19:19:36.054][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-10 19:19:36.056][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-10 19:19:36.057][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-10 19:19:36.058][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:19:36.060][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:19:36.061][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-10 19:19:36.062][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-10 19:19:36.064][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-10 19:19:36.065][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-10 19:19:36.067][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-10 19:19:36.068][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-10 19:19:36.069][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-10 19:19:36.071][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-10 19:19:36.072][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-10 19:19:36.074][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-10 19:19:36.075][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-10 19:19:36.076][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-10 19:19:36.078][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-10 19:19:36.079][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-10 19:19:36.081][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-10 19:19:36.082][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-10 19:19:36.084][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:19:36.085][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:36.086][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.088][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.145][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[2023-04-10 19:19:36.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:36.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:36.204][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-04-10 19:19:36.206][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-04-10 19:19:36.208][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:36.209][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-10 19:19:36.210][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:36.211][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:36.212][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:36.213][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-04-10 19:19:36.465][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:36.467][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:36.468][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-10 19:19:36.469][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:36.470][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:36.471][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-04-10 19:19:36.472][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-04-10 19:19:36.473][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-04-10 19:19:36.474][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:36.475][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:36.475][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-04-10 19:19:36.476][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-10 19:19:36.476][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:36.477][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:36.478][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:36.479][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:36.480][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:36.481][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:36.482][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-10 19:19:36.482][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-04-10 19:19:36.483][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:36.483][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:36.484][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:36.485][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:36.487][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:19:36.488][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:19:36.490][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:19:36.492][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:19:36.495][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-04-10 19:19:36.496][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-04-10 19:19:36.497][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-10 19:19:36.498][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-10 19:19:36.499][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:36.500][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:36.501][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-04-10 19:19:36.502][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-04-10 19:19:36.503][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-10 19:19:36.503][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-04-10 19:19:36.504][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:36.505][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:36.506][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-04-10 19:19:36.507][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-04-10 19:19:36.508][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-10 19:19:36.509][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-10 19:19:36.510][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:36.511][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:36.513][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-10 19:19:36.514][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:36.515][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-04-10 19:19:36.516][biodb::testThat]
biodb.INFO [2023-04-10 19:19:36.517][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2023-04-10 19:19:36.518][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:36.519][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:36.523][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:36.525][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:36.526][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-10 19:19:36.528][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:36.529][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-10 19:19:36.530][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-10 19:19:36.531][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-10 19:19:36.532][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-10 19:19:36.533][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-10 19:19:36.535][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2023-04-10 19:19:36.538][biodb::testThat]
biodb.INFO [2023-04-10 19:19:36.539][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2023-04-10 19:19:36.540][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:36.541][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:36.543][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-04-10 19:19:36.544][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-10 19:19:36.546][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:36.547][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-10 19:19:36.549][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-04-10 19:19:36.550][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:36.552][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-04-10 19:19:36.553][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:36.554][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:36.555][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-10 19:19:36.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:36.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:36.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:36.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:36.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:36.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:36.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:36.570][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.571][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.573][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.573][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.580][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:36.581][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:36.582][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.583][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.584][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:36.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:36.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.589][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:36.590][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:36.591][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.592][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.593][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:36.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:36.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.598][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.599][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.600][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.601][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.607][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:36.608][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:36.609][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.610][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:36.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:36.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.616][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:36.617][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:36.618][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.619][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.621][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:36.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:36.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.625][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:36.626][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:36.627][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.628][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.630][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:36.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:36.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.634][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:36.636][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:36.637][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.637][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.639][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:36.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:36.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.644][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:36.645][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:36.646][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.647][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.648][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:36.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:36.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.653][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:36.654][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:36.655][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.656][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.657][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:36.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:36.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.662][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:36.663][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:36.664][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.665][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:36.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:36.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.671][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.672][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.673][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.674][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.676][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.681][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:36.682][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:36.683][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.684][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:36.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:36.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.690][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:36.691][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:36.692][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.693][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:36.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:36.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.699][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:36.700][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:36.701][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.702][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.703][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:36.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:36.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.708][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:36.709][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:36.710][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.711][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.712][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:36.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:36.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.717][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-10 19:19:36.718][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:36.719][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.720][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.722][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-10 19:19:36.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:36.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:36.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:36.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.740][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:36.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:36.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.744][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:36.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:36.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.748][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:36.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:36.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.753][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:36.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:36.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.757][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:36.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:36.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.761][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:36.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:36.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:36.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:36.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:36.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:36.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:36.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:36.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:36.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.791][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:36.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:36.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.796][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:36.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:36.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.800][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:36.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:36.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.805][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:36.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:36.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.809][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:36.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:36.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.814][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:36.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:36.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.827][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:36.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:36.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.831][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:36.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:36.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.835][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:36.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:36.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.839][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:36.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:36.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.842][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:36.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:36.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.846][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:36.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:36.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.851][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:36.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:36.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.856][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:36.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:36.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.860][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:36.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:36.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:36.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:36.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:36.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:36.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:36.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:36.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.875][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.879][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.887][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:36.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:36.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.891][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:36.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:36.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.895][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:36.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:36.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:36.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:36.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:36.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:36.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:36.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:36.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.910][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:36.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:36.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.914][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:36.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:36.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:36.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:36.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.922][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:36.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:36.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.926][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:36.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:36.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.930][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:36.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:36.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.934][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:36.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:36.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.948][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:36.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:36.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.954][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:36.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:36.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.958][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-10 19:19:36.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.963][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.968][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.977][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-10 19:19:36.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:36.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:36.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:36.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:36.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:36.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.992][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:36.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:36.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.997][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:36.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:36.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.001][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:37.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:37.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.005][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:37.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:37.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.009][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:37.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:37.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.018][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:37.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:37.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:37.048][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-04-10 19:19:37.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:37.066][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-10 19:19:37.068][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-04-10 19:19:37.070][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-04-10 19:19:37.071][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-10 19:19:37.072][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.074][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.076][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-10 19:19:37.081][biodb::testContext]
biodb.INFO [2023-04-10 19:19:37.083][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:19:37.084][biodb::testContext] Test context - Test search of entries
biodb.INFO [2023-04-10 19:19:37.085][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:19:37.086][biodb::testContext]
biodb.INFO [2023-04-10 19:19:37.089][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:19:37.091][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-10 19:19:37.095][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:37.097][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-10 19:19:37.098][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-10 19:19:37.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.102][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-10 19:19:37.103][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-10 19:19:37.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.106][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-10 19:19:37.108][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-10 19:19:37.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.111][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-10 19:19:37.112][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-10 19:19:37.114][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-10 19:19:37.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.117][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-10 19:19:37.118][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-10 19:19:37.119][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-10 19:19:37.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.123][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-10 19:19:37.124][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-10 19:19:37.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.128][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-10 19:19:37.129][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-10 19:19:37.130][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-10 19:19:37.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.134][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-10 19:19:37.135][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-10 19:19:37.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.139][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-10 19:19:37.140][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-10 19:19:37.141][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-10 19:19:37.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.145][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:19:37.146][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-10 19:19:37.147][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-10 19:19:37.148][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-10 19:19:37.149][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-10 19:19:37.150][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-10 19:19:37.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.154][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-10 19:19:37.155][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-10 19:19:37.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.159][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-10 19:19:37.160][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-10 19:19:37.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.164][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-10 19:19:37.165][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-10 19:19:37.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.168][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-10 19:19:37.170][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-10 19:19:37.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.173][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-10 19:19:37.174][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-10 19:19:37.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.178][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:19:37.179][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-10 19:19:37.197][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-10 19:19:37.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.202][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-10 19:19:37.203][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-10 19:19:37.204][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-10 19:19:37.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.208][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-10 19:19:37.210][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.211][self$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[2023-04-10 19:19:37.212][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.213][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:37.214][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.216][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.217][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.218][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:19:37.219][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:37.220][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.221][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-10 19:19:37.221][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:37.222][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.223][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.224][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:37.224][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:19:37.224][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:19:37.224][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:19:37.224][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:19:37.225][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:37.226][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:37.227][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:37.228][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:37.229][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:37.230][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:37.231][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.232][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.233][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:37.234][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:37.235][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.236][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.237][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-10 19:19:37.239][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.240][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:19:37.241][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.242][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:37.243][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.244][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.245][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.246][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.247][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:19:37.248][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:37.249][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.250][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-10 19:19:37.251][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:37.252][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.253][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.254][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:37.254][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:19:37.254][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:19:37.254][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:19:37.254][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:19:37.255][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:37.256][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:37.257][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:37.258][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:37.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:37.260][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:37.261][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.261][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.262][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:37.263][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:37.264][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.266][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.267][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-10 19:19:37.269][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.270][self$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[2023-04-10 19:19:37.271][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.272][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:37.273][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.274][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.275][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.276][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.277][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:19:37.278][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:37.279][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.280][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-10 19:19:37.281][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:37.282][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.283][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.284][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.285][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:37.286][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:37.287][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:37.288][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:37.289][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:37.290][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:37.291][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.292][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.293][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:37.294][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:37.295][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.296][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.297][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-10 19:19:37.299][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.300][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:19:37.301][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.302][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:37.303][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.304][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.305][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.306][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.307][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:19:37.308][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:37.309][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.310][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-10 19:19:37.311][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:37.312][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.313][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.314][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.315][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:37.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:37.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:37.318][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:37.318][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:37.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:37.320][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.321][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.322][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:37.323][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:37.324][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.325][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.326][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:37.327][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.332][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[2023-04-10 19:19:37.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.344][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[2023-04-10 19:19:37.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.374][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[2023-04-10 19:19:37.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.401][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-10 19:19:37.402][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-10 19:19:37.404][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-10 19:19:37.405][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-10 19:19:37.406][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:19:37.408][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:19:37.409][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-10 19:19:37.410][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-10 19:19:37.412][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-10 19:19:37.413][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:19:37.414][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:19:37.416][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-10 19:19:37.417][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-10 19:19:37.418][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-10 19:19:37.420][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-10 19:19:37.421][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:19:37.422][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-10 19:19:37.424][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-10 19:19:37.425][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:19:37.426][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-10 19:19:37.427][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-10 19:19:37.429][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-10 19:19:37.430][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-10 19:19:37.431][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-10 19:19:37.433][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-10 19:19:37.434][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-10 19:19:37.435][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-10 19:19:37.437][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-10 19:19:37.438][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-10 19:19:37.439][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-10 19:19:37.441][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-10 19:19:37.442][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-10 19:19:37.443][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-10 19:19:37.444][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-10 19:19:37.446][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-10 19:19:37.447][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-10 19:19:37.448][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-10 19:19:37.449][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-10 19:19:37.451][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-10 19:19:37.452][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-10 19:19:37.453][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-10 19:19:37.455][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-10 19:19:37.456][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-10 19:19:37.458][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-10 19:19:37.459][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-10 19:19:37.460][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-10 19:19:37.461][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-10 19:19:37.463][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-10 19:19:37.464][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-10 19:19:37.465][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-10 19:19:37.467][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-10 19:19:37.468][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-10 19:19:37.469][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-10 19:19:37.471][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-10 19:19:37.472][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-10 19:19:37.473][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-10 19:19:37.474][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-10 19:19:37.476][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-10 19:19:37.477][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-10 19:19:37.478][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-10 19:19:37.480][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-10 19:19:37.481][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-10 19:19:37.483][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-10 19:19:37.484][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-10 19:19:37.485][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-10 19:19:37.487][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-10 19:19:37.488][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:19:37.490][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:19:37.491][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-10 19:19:37.492][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-10 19:19:37.494][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-10 19:19:37.495][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-10 19:19:37.496][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-10 19:19:37.498][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-10 19:19:37.499][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-10 19:19:37.500][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-10 19:19:37.508][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-10 19:19:37.509][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-10 19:19:37.511][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-10 19:19:37.512][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-10 19:19:37.513][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-10 19:19:37.514][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-10 19:19:37.516][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-10 19:19:37.517][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-10 19:19:37.519][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:19:37.520][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:37.520][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.522][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.523][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[2023-04-10 19:19:37.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.540][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[2023-04-10 19:19:37.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.588][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[2023-04-10 19:19:37.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.593][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.DEBUG[2023-04-10 19:19:37.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.599][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[2023-04-10 19:19:37.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.605][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[2023-04-10 19:19:37.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:37.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.617][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[2023-04-10 19:19:37.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:37.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.623][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[2023-04-10 19:19:37.624][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-04-10 19:19:37.625][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-04-10 19:19:37.627][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.628][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.629][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.630][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:37.631][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.632][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-04-10 19:19:37.633][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.634][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.634][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-10 19:19:37.635][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:37.636][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.637][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-04-10 19:19:37.638][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-04-10 19:19:37.639][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-04-10 19:19:37.640][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:37.641][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:37.641][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-04-10 19:19:37.642][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-10 19:19:37.643][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:37.644][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:37.645][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:37.646][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:37.647][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:37.647][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:37.648][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-10 19:19:37.648][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-04-10 19:19:37.649][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:37.650][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:37.651][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:37.652][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:37.653][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:19:37.655][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:19:37.656][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:19:37.658][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:19:37.661][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-04-10 19:19:37.662][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-04-10 19:19:37.663][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-10 19:19:37.665][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-10 19:19:37.666][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:37.667][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:37.668][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-04-10 19:19:37.669][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-04-10 19:19:37.670][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-10 19:19:37.670][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-04-10 19:19:37.671][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:37.672][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:37.673][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-04-10 19:19:37.673][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-04-10 19:19:37.675][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-10 19:19:37.676][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-10 19:19:37.677][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:37.678][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:37.679][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-10 19:19:37.681][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-10 19:19:37.681][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-04-10 19:19:37.683][biodb::testThat]
biodb.INFO [2023-04-10 19:19:37.684][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2023-04-10 19:19:37.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:37.686][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:37.688][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-04-10 19:19:37.689][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2023-04-10 19:19:37.690][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2023-04-10 19:19:37.693][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:37.694][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:37.696][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-10 19:19:37.697][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:37.698][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-10 19:19:37.699][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-10 19:19:37.700][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-10 19:19:37.701][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-10 19:19:37.702][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-10 19:19:37.703][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-10 19:19:37.704][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2023-04-10 19:19:37.706][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-04-10 19:19:37.707][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-10 19:19:37.709][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:37.710][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-10 19:19:37.712][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-04-10 19:19:37.713][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:37.715][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-04-10 19:19:37.716][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:37.717][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:37.718][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-10 19:19:37.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:37.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:37.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:37.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:37.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:37.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:37.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:37.735][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.736][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.737][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.738][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.744][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:37.745][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:37.746][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.747][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.748][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:37.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:37.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.752][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:37.754][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:37.754][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.755][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.757][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:37.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:37.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.761][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.762][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.763][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.764][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.769][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:37.770][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:37.771][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.772][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:37.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:37.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.778][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:37.779][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:37.780][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.780][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.782][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:37.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:37.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.786][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:37.787][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:37.788][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.789][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.790][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:37.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:37.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.794][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:37.795][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:37.796][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.797][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.798][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:37.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:37.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.802][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:37.803][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:37.804][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.805][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.806][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:37.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:37.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.810][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:37.811][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:37.812][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.813][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.814][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:37.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:37.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.818][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:37.824][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:37.825][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.826][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:37.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:37.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.831][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:37.832][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:37.833][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.834][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.835][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:37.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:37.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.839][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:37.840][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:37.841][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.842][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:37.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:37.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.847][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:37.848][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:37.849][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.850][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:37.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:37.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.855][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:37.856][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:37.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.858][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.859][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:37.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:37.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.863][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:37.864][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:37.864][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.865][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.867][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:37.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:37.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.871][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-10 19:19:37.872][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:37.873][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.874][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.875][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-10 19:19:37.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:37.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:37.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:37.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.890][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:37.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:37.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.894][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:37.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:37.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.898][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:37.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:37.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.901][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:37.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:37.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.905][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:37.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:37.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.909][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:37.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:37.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:37.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:37.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:37.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:37.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:37.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:37.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:37.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.935][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:37.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:37.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.939][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:37.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:37.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.943][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:37.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:37.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.947][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:37.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:37.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.950][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:37.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:37.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.954][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:37.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:37.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.958][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:37.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:37.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.962][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:37.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:37.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.966][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:37.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:37.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.969][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:37.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:37.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.973][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:37.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:37.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.977][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:37.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:37.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:37.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:37.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:37.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:37.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.988][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:37.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:37.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.992][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:37.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:37.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:37.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:37.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:38.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:38.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.007][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.015][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.018][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.022][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.045][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.049][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.052][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.056][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.060][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:38.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:38.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.064][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:38.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:38.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.068][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:38.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:38.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.071][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-10 19:19:38.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.086][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-10 19:19:38.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.091][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.095][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.099][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.106][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.110][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:38.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:38.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.114][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:38.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:38.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.121][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:38.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:38.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:38.152][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-04-10 19:19:38.153][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.157][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.161][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.164][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:38.168][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-10 19:19:38.169][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-10 19:19:38.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:38.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:38.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:38.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:38.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:38.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:38.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:38.181][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-04-10 19:19:38.182][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-10 19:19:38.184][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:38.185][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-10 19:19:38.187][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-04-10 19:19:38.188][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:38.190][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-04-10 19:19:38.191][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:38.192][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:38.193][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-10 19:19:38.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:38.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:38.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:38.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:38.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:38.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:38.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:38.208][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.209][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.210][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.211][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.216][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:38.217][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:38.218][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.219][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.220][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:38.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:38.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.224][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:38.225][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:38.226][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.227][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.229][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:38.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:38.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.232][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.233][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.234][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.235][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.241][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:38.242][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:38.242][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.243][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:38.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:38.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.249][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.250][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.251][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.252][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.253][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.257][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.258][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.259][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.260][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.261][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.265][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:38.266][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:38.267][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.268][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.269][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:38.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:38.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.273][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:38.274][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:38.275][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.276][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.277][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:38.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:38.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.281][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:38.282][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:38.283][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.284][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.285][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:38.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:38.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.289][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:38.290][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:38.291][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.291][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.293][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:38.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:38.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.297][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.298][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.299][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.299][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.305][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.306][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.306][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.307][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.313][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.314][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.314][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.315][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.317][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.320][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.321][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.322][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.323][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.325][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.329][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:38.330][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:38.330][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.331][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.333][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:38.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:38.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.337][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-10 19:19:38.338][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:38.338][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.339][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.341][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-10 19:19:38.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:38.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.356][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:38.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:38.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.360][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:38.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:38.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.363][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:38.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:38.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.367][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:38.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:38.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.371][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:38.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:38.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.374][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-10 19:19:38.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-10 19:19:38.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:38.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:38.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:38.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:38.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:38.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:38.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-10 19:19:38.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.402][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:38.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:38.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.405][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:38.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:38.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.409][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:38.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:38.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.413][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:38.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:38.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.416][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:38.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:38.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.420][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:38.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-10 19:19:38.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.424][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:38.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:38.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.427][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:38.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:38.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.431][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:38.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-10 19:19:38.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.435][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.438][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.448][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.451][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:38.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:38.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.455][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:38.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:38.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.458][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:38.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:38.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:38.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:38.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:38.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:38.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-10 19:19:38.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-10 19:19:38.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.481][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.484][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.488][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.492][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:38.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.518][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.521][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.525][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:38.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.529][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:38.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:38.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.532][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:38.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:38.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.536][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-10 19:19:38.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-10 19:19:38.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.540][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-10 19:19:38.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.555][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-10 19:19:38.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-10 19:19:38.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.567][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:38.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:38.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.578][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:38.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:38.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.582][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:38.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:38.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.589][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:38.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:38.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:38.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:38.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:38.615][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-04-10 19:19:38.616][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.620][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.624][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.628][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:38.631][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-10 19:19:38.632][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2023-04-10 19:19:38.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:38.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:38.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:38.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:38.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:38.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:38.643][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[2023-04-10 19:19:38.647][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-04-10 19:19:38.648][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-04-10 19:19:38.648][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-04-10 19:19:38.650][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:38.651][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:38.653][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-10 19:19:38.654][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:38.655][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-10 19:19:38.656][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-10 19:19:38.657][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-10 19:19:38.658][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-10 19:19:38.659][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-10 19:19:38.660][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-10 19:19:38.661][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-10 19:19:38.662][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.666][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.670][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.673][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.677][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.681][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.685][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:38.688][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-10 19:19:38.689][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-10 19:19:38.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:38.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:38.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:38.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:38.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:38.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:38.699][FUN] Functions in observer BiodbConfig: [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[2023-04-10 19:19:38.701][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.705][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.708][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.712][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.716][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.720][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.723][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:38.727][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-04-10 19:19:38.728][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-10 19:19:38.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:38.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:38.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:38.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:38.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:38.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:38.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:38.741][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-04-10 19:19:38.742][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-04-10 19:19:38.748][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-04-10 19:19:38.750][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:38.751][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:38.752][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-10 19:19:38.754][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-10 19:19:38.754][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-10 19:19:38.756][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-10 19:19:38.756][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-10 19:19:38.757][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-10 19:19:38.758][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-10 19:19:38.759][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-10 19:19:38.760][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-10 19:19:38.762][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.765][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.769][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.772][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.776][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.780][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.783][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:38.787][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-04-10 19:19:38.788][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2023-04-10 19:19:38.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:38.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:38.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:38.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:38.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:38.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:38.798][FUN] Functions in observer BiodbConfig: [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[2023-04-10 19:19:38.799][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.803][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.807][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.811][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.814][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.818][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.822][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-10 19:19:38.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-10 19:19:38.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:38.825][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-10 19:19:38.826][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-10 19:19:38.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:38.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:38.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:38.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:38.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:38.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:38.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-10 19:19:38.840][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-10 19:19:38.841][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-04-10 19:19:38.842][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-04-10 19:19:38.843][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-10 19:19:38.844][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:38.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:38.846][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:38.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:38.847][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:38.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 186 ]
>
> proc.time()
user system elapsed
9.088 0.333 10.764
biodbHmdb.Rcheck/biodbHmdb-Ex.timings
| name | user | system | elapsed | |
| HmdbMetabolitesConn | 1.695 | 0.099 | 1.796 | |
| HmdbMetabolitesEntry | 0.292 | 0.000 | 0.291 | |