| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:36 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 181/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbHmdb 1.5.0 (landing page) Pierrick Roger
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: biodbHmdb |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings biodbHmdb_1.5.0.tar.gz |
| StartedAt: 2023-02-27 21:52:56 -0000 (Mon, 27 Feb 2023) |
| EndedAt: 2023-02-27 21:54:25 -0000 (Mon, 27 Feb 2023) |
| EllapsedTime: 88.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbHmdb.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings biodbHmdb_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbHmdb.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
libs 5.9Mb
* 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 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-3.17-bioc/meat/biodbHmdb.Rcheck/00check.log’
for details.
biodbHmdb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL biodbHmdb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘biodbHmdb’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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-3.17-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-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2023-02-27 21:53:57.211][biodb::testContext]
biodb.INFO [2023-02-27 21:53:57.231][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-27 21:53:57.232][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2023-02-27 21:53:57.233][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-27 21:53:57.235][biodb::testContext]
biodb.INFO [2023-02-27 21:53:57.237][biodb::testThat]
biodb.INFO [2023-02-27 21:53:57.238][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2023-02-27 21:53:57.239][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:53:57.241][biodb::testThat]
biodb.INFO [2023-02-27 21:53:57.368][biodb::testContext]
biodb.INFO [2023-02-27 21:53:57.369][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-27 21:53:57.370][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-02-27 21:53:57.372][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-27 21:53:57.373][biodb::testContext]
biodb.INFO [2023-02-27 21:53:57.393][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-27 21:53:57.396][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-27 21:53:57.405][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-27 21:53:57.406][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-27 21:53:57.407][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-27 21:53:57.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.412][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-27 21:53:57.437][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-27 21:53:57.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.442][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-27 21:53:57.443][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-27 21:53:57.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.448][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-27 21:53:57.450][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-27 21:53:57.451][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-27 21:53:57.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.456][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-27 21:53:57.457][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-27 21:53:57.459][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-27 21:53:57.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.463][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-27 21:53:57.465][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-27 21:53:57.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.469][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-27 21:53:57.471][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-27 21:53:57.472][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-27 21:53:57.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.477][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-27 21:53:57.478][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-27 21:53:57.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.483][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-27 21:53:57.484][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-27 21:53:57.486][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-27 21:53:57.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.491][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-27 21:53:57.492][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-27 21:53:57.493][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-27 21:53:57.495][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-27 21:53:57.496][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-27 21:53:57.497][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-27 21:53:57.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.502][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-27 21:53:57.503][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-27 21:53:57.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.519][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-27 21:53:57.521][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-27 21:53:57.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.524][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[2023-02-27 21:53:57.526][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-27 21:53:57.527][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-27 21:53:57.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.532][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-27 21:53:57.534][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-27 21:53:57.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.539][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-27 21:53:57.540][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-27 21:53:57.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.545][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-27 21:53:57.547][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-27 21:53:57.551][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-27 21:53:57.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.556][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-27 21:53:57.557][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-27 21:53:57.559][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-27 21:53:57.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.568][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-27 21:53:57.615][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:57.636][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-02-27 21:53:57.638][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.639][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:53:57.641][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.642][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-27 21:53:57.643][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:57.644][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:53:57.646][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-27 21:53:57.647][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:53:57.648][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.650][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-27 21:53:57.651][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:53:57.652][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.653][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.655][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-27 21:53:57.655][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-27 21:53:57.655][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-27 21:53:57.655][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-27 21:53:57.655][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-27 21:53:57.656][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-27 21:53:57.657][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:53:57.658][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:53:57.660][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:53:57.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:53:57.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:53:57.663][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:53:57.665][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.666][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:53:57.667][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:53:57.668][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:57.669][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.671][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-27 21:53:57.673][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:57.675][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-27 21:53:57.676][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.677][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:53:57.678][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.680][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-27 21:53:57.681][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:57.682][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:53:57.684][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-27 21:53:57.685][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:53:57.686][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.687][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-27 21:53:57.689][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:53:57.690][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.691][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.692][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-27 21:53:57.692][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-27 21:53:57.692][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-27 21:53:57.692][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-27 21:53:57.692][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-27 21:53:57.694][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-27 21:53:57.695][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:53:57.696][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:53:57.697][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:53:57.699][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:53:57.700][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:53:57.701][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:53:57.702][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.704][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:53:57.705][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:53:57.706][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:57.707][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.709][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-27 21:53:57.711][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.712][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-02-27 21:53:57.714][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.715][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:53:57.716][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.717][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-27 21:53:57.719][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:57.720][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:53:57.721][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-27 21:53:57.723][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:53:57.724][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:57.725][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-27 21:53:57.726][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:53:57.728][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.729][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.730][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.732][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-27 21:53:57.733][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:53:57.734][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:53:57.735][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:53:57.736][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:53:57.738][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:53:57.739][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:53:57.740][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.741][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:53:57.742][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:53:57.744][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:57.745][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.747][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-27 21:53:57.749][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.750][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-27 21:53:57.761][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.762][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:53:57.764][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.765][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-27 21:53:57.766][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:57.768][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:53:57.769][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-27 21:53:57.770][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:53:57.772][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:57.773][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-27 21:53:57.775][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:53:57.776][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.777][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:57.779][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.780][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-27 21:53:57.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:53:57.783][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:53:57.784][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:53:57.785][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:53:57.787][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:53:57.788][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:53:57.789][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.791][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:53:57.792][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:53:57.793][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:57.794][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:57.800][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-27 21:53:57.801][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.815][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[2023-02-27 21:53:57.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.891][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[2023-02-27 21:53:57.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.896][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[2023-02-27 21:53:57.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:57.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:57.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:57.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:57.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:57.903][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-27 21:53:57.910][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-27 21:53:57.912][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-27 21:53:57.914][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-27 21:53:57.916][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-27 21:53:57.918][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-27 21:53:57.919][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-27 21:53:57.921][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-27 21:53:57.923][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-27 21:53:57.925][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-27 21:53:57.927][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-27 21:53:57.929][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-27 21:53:57.931][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-27 21:53:57.932][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-27 21:53:57.934][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-27 21:53:57.936][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-27 21:53:57.938][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-27 21:53:57.940][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-27 21:53:57.942][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-27 21:53:57.944][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-27 21:53:57.946][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-27 21:53:57.948][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-27 21:53:57.950][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-27 21:53:57.952][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-27 21:53:57.953][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-27 21:53:57.955][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-27 21:53:57.957][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-27 21:53:57.959][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-27 21:53:57.961][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-27 21:53:57.963][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-27 21:53:57.965][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-27 21:53:57.967][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-27 21:53:57.968][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-27 21:53:57.970][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-27 21:53:57.972][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-27 21:53:57.974][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-27 21:53:57.976][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-27 21:53:57.978][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-27 21:53:57.980][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-27 21:53:57.982][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-27 21:53:57.984][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-27 21:53:57.986][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-27 21:53:57.988][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-27 21:53:57.990][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-27 21:53:57.992][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-27 21:53:57.994][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-27 21:53:58.005][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-27 21:53:58.007][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-27 21:53:58.009][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-27 21:53:58.011][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-27 21:53:58.013][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-27 21:53:58.015][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-27 21:53:58.017][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-27 21:53:58.019][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-27 21:53:58.021][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-27 21:53:58.023][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-27 21:53:58.025][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-27 21:53:58.027][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-27 21:53:58.029][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-27 21:53:58.031][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-27 21:53:58.033][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-27 21:53:58.035][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-27 21:53:58.037][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-27 21:53:58.039][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-27 21:53:58.041][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-27 21:53:58.043][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-27 21:53:58.045][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-27 21:53:58.047][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-27 21:53:58.049][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-27 21:53:58.051][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-27 21:53:58.053][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-27 21:53:58.055][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-27 21:53:58.057][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-27 21:53:58.059][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-27 21:53:58.061][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-27 21:53:58.063][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-27 21:53:58.065][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-27 21:53:58.068][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-27 21:53:58.070][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-27 21:53:58.072][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-27 21:53:58.074][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-27 21:53:58.076][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-27 21:53:58.077][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-27 21:53:58.086][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-27 21:53:58.088][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-27 21:53:58.092][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-27 21:53:58.094][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.096][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.097][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[2023-02-27 21:53:58.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:58.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.120][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[2023-02-27 21:53:58.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:58.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:58.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:58.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:58.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.163][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[2023-02-27 21:53:58.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.172][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[2023-02-27 21:53:58.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.180][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[2023-02-27 21:53:58.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:58.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:58.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:58.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:58.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:58.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:58.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:58.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:53:58.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:53:58.290][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-02-27 21:53:58.303][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-02-27 21:53:58.306][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:58.308][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-27 21:53:58.309][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:58.311][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:53:58.312][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:58.313][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-02-27 21:53:58.315][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:58.316][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:53:58.318][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-27 21:53:58.319][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:53:58.320][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:58.322][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-02-27 21:53:58.323][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-02-27 21:53:58.325][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-02-27 21:53:58.326][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-27 21:53:58.328][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-27 21:53:58.328][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-02-27 21:53:58.329][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-27 21:53:58.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:53:58.332][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:53:58.333][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:53:58.334][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:53:58.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:53:58.337][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:53:58.338][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-02-27 21:53:58.338][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-02-27 21:53:58.340][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:53:58.341][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:53:58.342][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-27 21:53:58.344][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:53:58.352][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-27 21:53:58.354][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-27 21:53:58.356][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-27 21:53:58.359][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-27 21:53:58.391][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-02-27 21:53:58.392][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-02-27 21:53:58.398][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-02-27 21:53:58.403][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-27 21:53:58.409][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:53:58.410][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:53:58.412][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-02-27 21:53:58.414][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-02-27 21:53:58.415][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-02-27 21:53:58.415][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-02-27 21:53:58.416][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:53:58.418][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:53:58.419][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-02-27 21:53:58.420][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-02-27 21:53:58.421][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-02-27 21:53:58.445][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-27 21:53:58.447][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:53:58.448][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:53:58.450][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-27 21:53:58.452][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:53:58.453][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-02-27 21:53:58.473][biodb::testThat]
biodb.INFO [2023-02-27 21:53:58.475][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-02-27 21:53:58.476][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:53:58.477][biodb::testThat]
biodb.TRACE[2023-02-27 21:53:58.484][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2023-02-27 21:53:58.490][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-27 21:53:58.495][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-27 21:53:58.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-27 21:53:58.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:53:58.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:53:58.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:53:58.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:53:58.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:53:58.520][FUN] Functions in observer BiodbConfig: [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[2023-02-27 21:53:58.535][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:58.537][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:58.538][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.553][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:58.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:58.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.583][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:53:58.584][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:53:58.586][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.587][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.625][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:53:58.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:53:58.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.635][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:53:58.636][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:53:58.638][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.639][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.641][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:53:58.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:53:58.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.650][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:53:58.652][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:53:58.653][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.654][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:53:58.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:53:58.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.666][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:58.667][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:58.669][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.670][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:58.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:58.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.681][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:58.682][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:58.684][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.685][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.687][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:58.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:58.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.696][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:58.699][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:58.700][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.701][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.703][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:58.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:58.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.712][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:58.714][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:58.715][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.716][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.718][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:58.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:58.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.728][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:53:58.729][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:53:58.731][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.732][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.734][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:53:58.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:53:58.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.743][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:53:58.744][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:53:58.746][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.747][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.749][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:53:58.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:53:58.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.766][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:53:58.768][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:53:58.769][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.770][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.772][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:53:58.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:53:58.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.782][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:53:58.783][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:53:58.785][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.786][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:53:58.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:53:58.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.798][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:58.799][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:58.801][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.802][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:58.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:58.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.813][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:58.815][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:58.816][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.817][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:58.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:58.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.829][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:53:58.830][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:53:58.832][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.833][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.835][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:53:58.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:53:58.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.844][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:53:58.846][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:53:58.847][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.848][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.850][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:53:58.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:53:58.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.860][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-02-27 21:53:58.862][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:58.863][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.864][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.867][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-02-27 21:53:58.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:58.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:58.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:58.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:58.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:58.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:58.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:58.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.939][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:53:58.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:53:58.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.945][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:53:58.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:53:58.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.951][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:53:58.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:53:58.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.966][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:53:58.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:53:58.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.972][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:53:58.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:53:58.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.978][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:53:58.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:53:58.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:53:58.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:53:58.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:53:58.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:53:58.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:58.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:58.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:53:58.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:53:58.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.018][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.024][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.030][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.035][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:53:59.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:53:59.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.041][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:53:59.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:53:59.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.046][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:53:59.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:53:59.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.051][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.057][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.062][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.068][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:53:59.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:53:59.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.073][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:53:59.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:53:59.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.078][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:53:59.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:53:59.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.084][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:53:59.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:53:59.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.089][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:53:59.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:53:59.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.094][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:53:59.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:53:59.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.100][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:53:59.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:53:59.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.105][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:53:59.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:53:59.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:53:59.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:53:59.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.121][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.127][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.132][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.138][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.143][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:59.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:59.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.178][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:59.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:59.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:59.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:59.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.189][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.195][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.201][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.206][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:53:59.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:53:59.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.212][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:53:59.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:53:59.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.217][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:53:59.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:53:59.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.223][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-27 21:53:59.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.228][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.234][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.239][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.245][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-27 21:53:59.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:53:59.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:59.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:59.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.284][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:59.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:59.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:59.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:59.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.295][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:59.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:59.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.300][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:59.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:59.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.309][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.315][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.325][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:53:59.376][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2023-02-27 21:53:59.383][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-27 21:53:59.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-27 21:53:59.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.389][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-27 21:53:59.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-27 21:53:59.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.395][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-27 21:53:59.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-27 21:53:59.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.400][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-27 21:53:59.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-27 21:53:59.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.438][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.484][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.490][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.495][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:53:59.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.527][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.529][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.530][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.531][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:53:59.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:53:59.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.564][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.565][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.567][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.568][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:53:59.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.594][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.600][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.606][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.612][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.613][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.615][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.616][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.617][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:53:59.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:53:59.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:53:59.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:53:59.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:53:59.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:53:59.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:53:59.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.652][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:53:59.653][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:53:59.655][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.656][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:53:59.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:53:59.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.673][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.679][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.684][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.690][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.691][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.693][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.694][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.695][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:53:59.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:59.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:59.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:59.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:59.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:59.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:59.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.728][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:59.730][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:59.731][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.733][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:53:59.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:53:59.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.750][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:53:59.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:53:59.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.756][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:53:59.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:53:59.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.762][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:53:59.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:53:59.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.769][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:53:59.771][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:53:59.772][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.774][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.775][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:53:59.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:53:59.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.799][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:53:59.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:53:59.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.805][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:53:59.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:53:59.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.810][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:53:59.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:53:59.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.816][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:53:59.817][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:53:59.819][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.820][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:53:59.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:53:59.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.837][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:53:59.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:53:59.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.843][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:53:59.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:53:59.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.849][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:53:59.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:53:59.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.854][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:53:59.856][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:53:59.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.859][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.860][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:53:59.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:53:59.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.892][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.893][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.895][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.896][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:53:59.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.912][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.918][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.923][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.928][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.930][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.931][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.932][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.934][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:53:59.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.949][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.954][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.959][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.964][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.966][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.967][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.968][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.970][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:53:59.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.984][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:53:59.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:53:59.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:53:59.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:53:59.998][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:53:59.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.003][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.009][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.010][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.012][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.013][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.014][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.029][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:00.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:00.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.035][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:00.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:00.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.041][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:00.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:00.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.046][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:00.047][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:00.049][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.050][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.051][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:00.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:00.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:00.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:00.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:00.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:00.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:00.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:00.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.082][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:00.084][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:00.085][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.086][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.088][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:00.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:00.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.118][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.120][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.121][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.122][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.138][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.143][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.149][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.154][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.155][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.156][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.158][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.159][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.174][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:00.175][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:00.177][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.178][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.193][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:00.195][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:00.196][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.198][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.205][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.207][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.208][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.210][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.217][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:00.219][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:00.220][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.221][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.230][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:00.231][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:00.233][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.235][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.243][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:00.244][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:00.245][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.247][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.254][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.256][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.257][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.258][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.266][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:00.268][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:00.269][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.270][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.278][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:00.280][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:00.281][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.282][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.290][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:00.292][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:00.293][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.294][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.302][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:00.303][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:00.305][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.306][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.314][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.315][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.317][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.318][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.326][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:00.327][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:00.328][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.330][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.337][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:00.339][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:00.340][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.342][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.349][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:00.351][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:00.352][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.354][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.361][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:00.363][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:00.364][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.365][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.373][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:00.375][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:00.376][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.377][ef$get] fields variable is a list.
biodb.INFO [2023-02-27 21:54:00.386][biodb::testThat]
biodb.INFO [2023-02-27 21:54:00.387][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-02-27 21:54:00.396][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:00.398][biodb::testThat]
biodb.DEBUG[2023-02-27 21:54:00.417][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-02-27 21:54:00.427][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-02-27 21:54:00.435][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:00.437][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-02-27 21:54:00.440][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-02-27 21:54:00.442][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-27 21:54:00.447][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-02-27 21:54:00.448][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-02-27 21:54:00.506][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-27 21:54:00.508][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-27 21:54:00.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-27 21:54:00.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:00.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:00.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:00.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:00.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:00.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-27 21:54:00.529][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:00.531][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:00.532][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.533][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:00.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:00.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.545][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:00.546][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:00.547][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.549][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.551][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:00.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:00.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.560][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.562][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.563][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.564][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.566][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.576][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:00.577][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:00.579][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.580][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:00.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:00.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.592][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:00.593][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:00.603][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.605][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:00.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:00.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.616][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:00.618][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:00.619][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.621][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.623][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:00.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:00.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.632][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:00.634][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:00.635][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.636][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.638][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:00.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:00.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.649][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:00.650][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:00.652][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.653][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.655][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:00.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:00.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.664][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.666][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.667][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.669][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.671][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.688][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:00.692][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:00.694][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.696][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.699][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:00.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:00.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.715][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:00.718][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:00.720][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.721][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.725][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:00.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:00.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.738][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.740][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.742][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.744][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.746][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:00.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.759][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:00.761][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:00.763][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.765][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:00.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:00.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.780][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:00.782][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:00.784][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.786][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:00.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:00.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.800][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:00.802][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:00.804][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.806][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.808][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:00.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:00.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.821][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:00.823][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:00.825][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.827][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.830][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:00.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:00.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.843][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-02-27 21:54:00.845][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:00.847][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.849][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.852][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-02-27 21:54:00.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:00.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:00.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:00.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:00.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:00.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:00.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:00.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.905][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:00.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:00.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.911][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:00.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:00.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.916][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:00.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:00.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.922][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.928][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.934][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:00.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:00.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:00.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:00.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:00.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:00.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:00.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:00.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:00.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:00.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:00.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:00.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:00.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.976][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:00.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:00.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.982][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:00.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:00.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.987][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:00.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:00.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.992][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:00.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:00.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:00.998][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:01.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:01.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.003][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:01.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:01.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.009][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:01.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:01.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.014][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:01.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:01.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.020][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:01.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:01.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.025][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:01.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:01.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.031][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:01.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:01.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.036][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:01.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:01.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.041][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:01.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:01.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.047][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:01.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:01.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.054][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:01.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:01.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:01.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:01.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:01.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:01.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.071][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:01.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:01.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.076][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.089][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.095][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.100][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:01.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:01.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.106][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:01.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:01.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.111][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:01.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:01.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:01.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:01.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:01.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:01.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:01.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:01.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.149][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:01.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:01.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.155][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:01.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:01.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.160][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:01.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:01.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.166][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:01.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:01.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.171][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:01.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:01.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.177][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:01.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:01.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.182][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-27 21:54:01.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.199][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.204][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-27 21:54:01.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:01.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.215][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.220][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.246][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:01.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:01.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.252][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:01.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:01.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:01.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:01.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.264][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:01.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:01.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:01.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:01.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:01.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:01.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:01.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:01.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:01.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:01.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:01.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:01.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:01.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:01.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:01.316][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-02-27 21:54:01.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-02-27 21:54:01.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-02-27 21:54:01.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-02-27 21:54:01.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-02-27 21:54:01.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-02-27 21:54:01.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-02-27 21:54:01.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-27 21:54:01.343][biodb::testThat]
biodb.INFO [2023-02-27 21:54:01.344][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-02-27 21:54:01.346][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:01.347][biodb::testThat]
biodb.TRACE[2023-02-27 21:54:01.351][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.353][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.354][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.355][ef$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:01.357][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2023-02-27 21:54:01.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:01.415][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2023-02-27 21:54:01.428][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-02-27 21:54:01.429][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-02-27 21:54:01.430][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-02-27 21:54:01.433][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:01.435][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:01.437][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-27 21:54:01.438][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:01.440][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-27 21:54:01.445][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-27 21:54:01.447][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-27 21:54:01.448][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-27 21:54:01.450][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-27 21:54:01.451][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-02-27 21:54:01.453][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-02-27 21:54:01.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.461][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.468][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:01.487][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-27 21:54:01.489][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-02-27 21:54:01.490][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2023-02-27 21:54:01.509][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:01.511][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:01.512][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.514][ef$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:01.515][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2023-02-27 21:54:01.535][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:01.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:01.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.541][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:01.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:01.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.546][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:01.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:01.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:01.553][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[2023-02-27 21:54:01.640][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-02-27 21:54:01.642][private$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[2023-02-27 21:54:01.643][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2023-02-27 21:54:01.672][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:01.674][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:01.676][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-27 21:54:01.678][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:01.679][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-27 21:54:01.704][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-27 21:54:01.706][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-27 21:54:01.707][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-27 21:54:01.708][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-27 21:54:01.710][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-02-27 21:54:01.711][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-02-27 21:54:01.713][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:01.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:01.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.719][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:01.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:01.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.724][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:01.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:01.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.729][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:01.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:01.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:01.735][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-27 21:54:01.736][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-02-27 21:54:01.737][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2023-02-27 21:54:01.758][biodb::testThat]
biodb.INFO [2023-02-27 21:54:01.759][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-02-27 21:54:01.761][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:01.762][biodb::testThat]
biodb.TRACE[2023-02-27 21:54:01.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:01.824][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-02-27 21:54:01.826][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-02-27 21:54:01.827][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-02-27 21:54:01.837][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:01.839][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:01.841][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-27 21:54:01.843][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:01.844][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-27 21:54:01.849][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-27 21:54:01.851][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-27 21:54:01.852][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-27 21:54:01.854][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-27 21:54:01.855][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-02-27 21:54:01.856][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-02-27 21:54:01.859][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.864][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.870][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.876][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:01.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:01.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:01.881][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-27 21:54:01.882][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2023-02-27 21:54:01.903][biodb::testThat]
biodb.INFO [2023-02-27 21:54:01.905][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-02-27 21:54:01.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:01.907][biodb::testThat]
biodb.TRACE[2023-02-27 21:54:01.943][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-27 21:54:01.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-27 21:54:01.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.948][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-27 21:54:01.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-27 21:54:01.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.954][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-27 21:54:01.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-27 21:54:01.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:01.959][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-27 21:54:01.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-27 21:54:01.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:01.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:02.049][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-27 21:54:02.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-27 21:54:02.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:02.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:02.055][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-27 21:54:02.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-27 21:54:02.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:02.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:02.061][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-27 21:54:02.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-27 21:54:02.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:02.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:02.067][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-27 21:54:02.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-27 21:54:02.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:02.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-27 21:54:02.077][biodb::testThat]
biodb.INFO [2023-02-27 21:54:02.078][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-02-27 21:54:02.080][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:02.081][biodb::testThat]
biodb.INFO [2023-02-27 21:54:02.088][biodb::testThat]
biodb.INFO [2023-02-27 21:54:02.089][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-02-27 21:54:02.091][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:02.092][biodb::testThat]
biodb.INFO [2023-02-27 21:54:02.099][biodb::testThat]
biodb.INFO [2023-02-27 21:54:02.100][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-02-27 21:54:02.102][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:02.103][biodb::testThat]
biodb.DEBUG[2023-02-27 21:54:02.108][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2023-02-27 21:54:04.672][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2023-02-27 21:54:05.185][biodb::testThat]
biodb.INFO [2023-02-27 21:54:05.187][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-02-27 21:54:05.188][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:05.189][biodb::testThat]
biodb.DEBUG[2023-02-27 21:54:06.810][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2023-02-27 21:54:07.326][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:07.327][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:07.329][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.330][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.331][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:07.333][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:07.334][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.335][ef$get] fields variable is a list.
biodb.INFO [2023-02-27 21:54:07.337][biodb::testThat]
biodb.INFO [2023-02-27 21:54:07.338][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-02-27 21:54:07.340][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:07.341][biodb::testThat]
biodb.DEBUG[2023-02-27 21:54:07.344][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-02-27 21:54:07.424][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-02-27 21:54:07.427][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:07.429][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-02-27 21:54:07.453][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-02-27 21:54:07.454][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-27 21:54:07.456][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-27 21:54:07.457][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-02-27 21:54:07.459][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:07.481][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-27 21:54:07.482][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-27 21:54:07.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-27 21:54:07.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:07.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:07.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:07.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:07.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:07.499][FUN] Functions in observer BiodbConfig: [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[2023-02-27 21:54:07.502][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:07.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:07.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.552][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:07.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:07.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:07.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:07.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:07.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:07.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:07.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:07.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:07.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:07.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:07.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:07.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:07.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:07.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:07.592][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-02-27 21:54:07.593][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-02-27 21:54:07.614][biodb::testThat]
biodb.INFO [2023-02-27 21:54:07.615][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-02-27 21:54:07.617][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:07.618][biodb::testThat]
biodb.DEBUG[2023-02-27 21:54:07.627][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2023-02-27 21:54:07.629][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2023-02-27 21:54:07.630][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-02-27 21:54:07.633][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:07.635][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-02-27 21:54:07.637][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2023-02-27 21:54:07.639][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-27 21:54:07.641][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-27 21:54:07.642][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-02-27 21:54:07.644][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:07.666][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-27 21:54:07.668][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-27 21:54:07.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-27 21:54:07.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:07.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:07.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:07.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:07.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:07.684][FUN] Functions in observer BiodbConfig: [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[2023-02-27 21:54:07.687][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:07.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:07.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.692][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:07.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:07.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:07.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:07.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:07.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:07.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:07.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:07.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:07.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:07.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:07.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:07.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:07.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:07.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:07.740][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-02-27 21:54:07.741][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-02-27 21:54:07.743][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2023-02-27 21:54:07.759][biodb::testThat]
biodb.INFO [2023-02-27 21:54:07.760][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-02-27 21:54:07.762][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:07.763][biodb::testThat]
biodb.INFO [2023-02-27 21:54:07.790][biodb::testThat]
biodb.INFO [2023-02-27 21:54:07.792][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-02-27 21:54:07.793][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:07.794][biodb::testThat]
biodb.DEBUG[2023-02-27 21:54:07.798][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:07.800][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:07.802][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-27 21:54:07.804][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:07.805][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-27 21:54:07.811][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-27 21:54:07.812][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-27 21:54:07.814][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-27 21:54:07.815][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2023-02-27 21:54:07.824][biodb::testThat]
biodb.INFO [2023-02-27 21:54:07.825][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-02-27 21:54:07.826][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:07.828][biodb::testThat]
biodb.DEBUG[2023-02-27 21:54:07.831][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:07.833][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:07.835][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-27 21:54:07.837][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:07.839][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-27 21:54:07.844][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-27 21:54:07.846][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-27 21:54:07.847][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-27 21:54:07.848][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2023-02-27 21:54:07.883][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:07.886][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:07.887][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.889][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:07.890][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:07.892][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:07.893][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:07.894][ef$get] fields variable is a list.
biodb.INFO [2023-02-27 21:54:07.896][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-27 21:54:07.898][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-02-27 21:54:07.910][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-02-27 21:54:07.912][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-27 21:54:07.913][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:07.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:07.916][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:07.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:07.919][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:07.920][FUN] Functions in observer BiodbConfig: [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 [2023-02-27 21:54:07.926][biodb::testContext]
biodb.INFO [2023-02-27 21:54:07.927][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-27 21:54:07.929][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2023-02-27 21:54:07.930][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-27 21:54:07.932][biodb::testContext]
biodb.INFO [2023-02-27 21:54:07.940][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-27 21:54:07.942][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-27 21:54:07.948][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-27 21:54:07.949][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-27 21:54:07.951][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-27 21:54:07.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:07.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:07.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:07.956][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-27 21:54:07.958][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-27 21:54:07.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:07.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:07.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:07.963][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-27 21:54:07.965][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-27 21:54:07.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:07.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:07.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:07.970][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-27 21:54:07.972][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-27 21:54:07.973][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-27 21:54:07.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:07.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:07.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:07.979][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-27 21:54:07.980][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-27 21:54:07.982][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-27 21:54:07.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:07.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:07.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:07.987][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-27 21:54:07.989][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-27 21:54:07.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:07.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:07.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:07.994][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-27 21:54:07.995][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-27 21:54:07.997][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-27 21:54:07.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.002][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-27 21:54:08.004][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-27 21:54:08.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.009][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-27 21:54:08.011][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-27 21:54:08.012][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-27 21:54:08.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.018][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-27 21:54:08.019][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-27 21:54:08.021][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-27 21:54:08.022][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-27 21:54:08.023][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-27 21:54:08.025][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-27 21:54:08.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.029][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[2023-02-27 21:54:08.030][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-27 21:54:08.032][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-27 21:54:08.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.037][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-27 21:54:08.039][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-27 21:54:08.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.055][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-27 21:54:08.057][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-27 21:54:08.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.062][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-27 21:54:08.064][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-27 21:54:08.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.069][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-27 21:54:08.070][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-27 21:54:08.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.075][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-27 21:54:08.077][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-27 21:54:08.081][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-27 21:54:08.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.086][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-27 21:54:08.087][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-27 21:54:08.089][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-27 21:54:08.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.094][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-27 21:54:08.097][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.098][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-02-27 21:54:08.100][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.101][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:54:08.102][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.104][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.105][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.106][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.108][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-27 21:54:08.109][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:54:08.111][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.112][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-27 21:54:08.113][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:54:08.115][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.116][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.117][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-27 21:54:08.117][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-27 21:54:08.117][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-27 21:54:08.117][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-27 21:54:08.117][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-27 21:54:08.119][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-27 21:54:08.120][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:08.121][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:08.123][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:54:08.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:08.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:08.127][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.128][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.129][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:54:08.131][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:54:08.132][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.133][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.135][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-27 21:54:08.138][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.139][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-27 21:54:08.140][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.142][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:54:08.143][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.145][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.146][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.147][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.149][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-27 21:54:08.150][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:54:08.152][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.153][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-27 21:54:08.154][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:54:08.156][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.157][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.159][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-27 21:54:08.159][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-27 21:54:08.159][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-27 21:54:08.159][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-27 21:54:08.159][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-27 21:54:08.160][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-27 21:54:08.161][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:08.163][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:08.164][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:54:08.165][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:08.166][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:08.168][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.169][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.171][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:54:08.172][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:54:08.173][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.175][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.177][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-27 21:54:08.179][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.180][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-02-27 21:54:08.182][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.183][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:54:08.185][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.186][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.188][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.189][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.190][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-27 21:54:08.192][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:54:08.193][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.195][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-27 21:54:08.196][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:54:08.197][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.199][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.200][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.202][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-27 21:54:08.203][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:08.204][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:08.206][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:54:08.207][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:08.216][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:08.218][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.219][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.220][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:54:08.222][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:54:08.223][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.224][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.226][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-27 21:54:08.229][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.230][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-27 21:54:08.231][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.233][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:54:08.234][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.236][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.237][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.238][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.240][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-27 21:54:08.241][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:54:08.243][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.244][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-27 21:54:08.245][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:54:08.247][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.248][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.249][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.251][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-27 21:54:08.252][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:08.253][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:08.255][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:54:08.256][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:08.257][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:08.259][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.260][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.262][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:54:08.263][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:54:08.264][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.266][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.268][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-27 21:54:08.269][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.332][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[2023-02-27 21:54:08.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.357][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[2023-02-27 21:54:08.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.378][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[2023-02-27 21:54:08.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.386][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-27 21:54:08.388][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-27 21:54:08.390][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-27 21:54:08.392][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-27 21:54:08.394][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-27 21:54:08.396][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-27 21:54:08.398][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-27 21:54:08.400][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-27 21:54:08.402][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-27 21:54:08.404][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-27 21:54:08.406][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-27 21:54:08.407][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-27 21:54:08.409][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-27 21:54:08.411][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-27 21:54:08.413][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-27 21:54:08.415][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-27 21:54:08.417][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-27 21:54:08.419][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-27 21:54:08.421][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-27 21:54:08.423][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-27 21:54:08.425][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-27 21:54:08.427][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-27 21:54:08.429][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-27 21:54:08.431][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-27 21:54:08.433][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-27 21:54:08.435][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-27 21:54:08.437][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-27 21:54:08.439][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-27 21:54:08.441][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-27 21:54:08.443][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-27 21:54:08.445][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-27 21:54:08.447][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-27 21:54:08.449][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-27 21:54:08.450][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-27 21:54:08.452][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-27 21:54:08.454][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-27 21:54:08.456][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-27 21:54:08.458][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-27 21:54:08.460][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-27 21:54:08.462][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-27 21:54:08.464][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-27 21:54:08.466][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-27 21:54:08.468][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-27 21:54:08.470][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-27 21:54:08.472][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-27 21:54:08.474][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-27 21:54:08.476][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-27 21:54:08.478][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-27 21:54:08.480][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-27 21:54:08.482][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-27 21:54:08.484][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-27 21:54:08.486][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-27 21:54:08.488][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-27 21:54:08.490][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-27 21:54:08.492][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-27 21:54:08.494][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-27 21:54:08.496][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-27 21:54:08.498][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-27 21:54:08.500][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-27 21:54:08.502][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-27 21:54:08.503][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-27 21:54:08.505][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-27 21:54:08.507][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-27 21:54:08.509][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-27 21:54:08.511][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-27 21:54:08.513][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-27 21:54:08.515][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-27 21:54:08.526][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-27 21:54:08.528][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-27 21:54:08.530][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-27 21:54:08.532][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-27 21:54:08.534][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-27 21:54:08.536][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-27 21:54:08.539][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-27 21:54:08.541][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-27 21:54:08.543][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-27 21:54:08.545][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-27 21:54:08.547][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-27 21:54:08.549][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-27 21:54:08.551][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-27 21:54:08.553][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-27 21:54:08.555][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-27 21:54:08.557][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-27 21:54:08.559][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-27 21:54:08.561][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-27 21:54:08.562][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-27 21:54:08.564][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.566][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.567][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.DEBUG[2023-02-27 21:54:08.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.576][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[2023-02-27 21:54:08.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.585][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[2023-02-27 21:54:08.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.611][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[2023-02-27 21:54:08.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:08.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:08.728][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-02-27 21:54:08.730][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-02-27 21:54:08.733][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.734][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.736][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.737][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:54:08.738][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.740][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-02-27 21:54:08.741][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.742][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.744][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-27 21:54:08.745][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:54:08.747][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.748][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-02-27 21:54:08.749][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-02-27 21:54:08.751][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-02-27 21:54:08.752][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:08.754][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-27 21:54:08.754][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-02-27 21:54:08.755][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-27 21:54:08.756][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:08.758][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:08.759][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:54:08.760][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:08.761][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:08.763][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:54:08.764][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-02-27 21:54:08.764][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-02-27 21:54:08.766][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:54:08.767][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:54:08.768][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:08.770][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:08.771][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-27 21:54:08.774][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-27 21:54:08.776][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-27 21:54:08.778][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-27 21:54:08.782][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-02-27 21:54:08.784][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-02-27 21:54:08.785][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-02-27 21:54:08.787][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-27 21:54:08.790][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:54:08.791][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:54:08.793][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-02-27 21:54:08.794][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-02-27 21:54:08.795][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-02-27 21:54:08.795][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-02-27 21:54:08.797][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:54:08.798][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:54:08.799][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-02-27 21:54:08.801][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-02-27 21:54:08.802][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-02-27 21:54:08.804][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-27 21:54:08.806][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:54:08.807][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:54:08.809][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-27 21:54:08.811][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:54:08.812][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-02-27 21:54:08.814][biodb::testThat]
biodb.INFO [2023-02-27 21:54:08.815][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2023-02-27 21:54:08.816][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:08.818][biodb::testThat]
biodb.DEBUG[2023-02-27 21:54:08.823][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:08.825][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:08.827][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-27 21:54:08.837][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:08.839][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-27 21:54:08.845][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-27 21:54:08.846][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-27 21:54:08.847][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-27 21:54:08.849][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-27 21:54:08.852][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2023-02-27 21:54:08.855][biodb::testThat]
biodb.INFO [2023-02-27 21:54:08.857][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2023-02-27 21:54:08.858][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:08.859][biodb::testThat]
biodb.DEBUG[2023-02-27 21:54:08.862][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-02-27 21:54:08.864][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-02-27 21:54:08.866][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:08.868][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-02-27 21:54:08.871][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-02-27 21:54:08.872][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-27 21:54:08.875][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-02-27 21:54:08.877][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-02-27 21:54:08.898][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-27 21:54:08.899][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-27 21:54:08.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-27 21:54:08.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:08.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:08.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:08.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:08.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:08.916][FUN] Functions in observer BiodbConfig: [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[2023-02-27 21:54:08.920][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:08.922][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:08.923][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:08.925][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:08.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:08.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:08.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:08.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:08.936][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:08.937][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:08.939][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:08.940][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:08.942][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:08.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:08.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:08.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:08.951][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:08.953][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:08.954][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:08.955][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:08.957][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:08.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:08.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:08.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:08.967][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:08.968][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:08.970][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:08.971][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:08.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:08.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:08.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:08.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:08.982][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:08.984][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:08.985][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:08.986][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:08.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:08.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:08.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:08.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.007][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:09.009][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:09.010][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.012][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.014][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:09.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:09.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.023][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:09.024][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:09.026][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.027][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.029][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:09.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:09.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.038][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:09.040][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:09.041][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.043][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.045][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:09.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:09.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.054][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:09.056][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:09.057][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.058][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.060][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:09.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:09.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.070][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:09.071][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:09.073][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.074][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.076][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:09.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:09.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.085][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:09.087][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:09.088][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.089][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.091][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:09.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:09.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.101][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.102][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.103][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.105][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.116][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:09.118][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:09.119][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.121][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:09.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:09.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.132][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:09.134][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:09.135][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.136][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:09.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:09.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.147][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:09.149][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:09.150][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.152][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.153][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:09.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:09.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.171][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:09.173][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:09.174][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.176][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.178][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:09.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:09.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.193][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-02-27 21:54:09.195][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:09.197][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.199][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.201][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-02-27 21:54:09.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:09.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:09.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:09.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:09.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:09.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:09.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:09.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.232][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:09.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:09.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.238][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:09.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:09.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.244][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:09.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:09.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.250][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:09.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:09.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.256][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:09.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:09.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.263][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:09.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:09.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:09.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:09.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:09.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:09.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:09.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:09.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:09.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:09.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:09.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:09.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:09.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:09.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.306][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:09.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:09.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:09.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:09.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.319][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:09.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:09.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.325][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:09.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:09.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.331][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:09.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:09.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.337][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:09.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:09.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.358][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:09.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:09.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.364][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:09.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:09.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.370][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:09.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:09.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.375][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:09.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:09.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.381][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:09.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:09.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.387][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:09.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:09.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.392][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:09.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:09.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.398][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:09.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:09.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.404][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:09.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:09.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:09.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:09.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.416][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:09.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:09.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:09.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:09.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.427][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.438][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.444][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:09.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:09.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.450][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:09.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:09.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.455][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:09.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:09.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:09.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:09.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:09.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:09.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:09.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:09.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:09.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:09.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.484][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:09.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:09.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:09.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:09.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.496][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:09.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:09.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.501][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:09.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:09.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.515][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:09.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:09.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.521][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:09.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:09.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.527][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:09.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:09.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.533][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:09.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:09.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.538][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-27 21:54:09.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.561][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-27 21:54:09.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:09.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.572][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:09.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:09.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.578][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:09.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:09.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:09.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:09.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:09.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:09.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.595][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:09.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:09.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.605][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:09.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:09.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.610][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:09.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:09.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:09.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:09.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.622][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:09.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:09.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:09.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:09.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:09.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:09.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:09.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:09.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:09.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:09.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:09.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:09.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:09.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:09.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:09.675][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-02-27 21:54:09.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:09.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:09.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:09.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:09.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:09.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:09.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:09.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:09.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-27 21:54:09.697][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-27 21:54:09.699][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-02-27 21:54:09.700][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-02-27 21:54:09.702][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-27 21:54:09.703][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:09.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:09.705][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:09.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:09.708][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-27 21:54:09.715][biodb::testContext]
biodb.INFO [2023-02-27 21:54:09.716][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-27 21:54:09.717][biodb::testContext] Test context - Test search of entries
biodb.INFO [2023-02-27 21:54:09.719][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-27 21:54:09.720][biodb::testContext]
biodb.INFO [2023-02-27 21:54:09.728][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-27 21:54:09.730][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-27 21:54:09.735][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-27 21:54:09.737][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-27 21:54:09.738][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-27 21:54:09.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.743][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-27 21:54:09.745][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-27 21:54:09.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.750][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-27 21:54:09.752][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-27 21:54:09.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.757][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-27 21:54:09.758][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-27 21:54:09.760][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-27 21:54:09.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.765][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-27 21:54:09.766][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-27 21:54:09.768][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-27 21:54:09.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.771][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[2023-02-27 21:54:09.773][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-27 21:54:09.774][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-27 21:54:09.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.779][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-27 21:54:09.781][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-27 21:54:09.782][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-27 21:54:09.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.787][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-27 21:54:09.789][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-27 21:54:09.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.794][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-27 21:54:09.795][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-27 21:54:09.797][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-27 21:54:09.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.802][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-27 21:54:09.804][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-27 21:54:09.805][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-27 21:54:09.807][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-27 21:54:09.808][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-27 21:54:09.809][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-27 21:54:09.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.815][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-27 21:54:09.816][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-27 21:54:09.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.821][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-27 21:54:09.823][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-27 21:54:09.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.836][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-27 21:54:09.838][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-27 21:54:09.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.843][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-27 21:54:09.845][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-27 21:54:09.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.850][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-27 21:54:09.851][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-27 21:54:09.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.856][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-27 21:54:09.858][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-27 21:54:09.862][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-27 21:54:09.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.868][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-27 21:54:09.869][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-27 21:54:09.871][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-27 21:54:09.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:09.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:09.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:09.876][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-27 21:54:09.879][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:09.880][self$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[2023-02-27 21:54:09.881][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:09.883][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:54:09.884][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:09.886][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-27 21:54:09.887][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:09.888][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:54:09.890][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-27 21:54:09.891][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:54:09.893][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:09.894][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-27 21:54:09.896][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:54:09.897][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:09.898][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:09.900][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-27 21:54:09.900][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-27 21:54:09.900][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-27 21:54:09.900][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-27 21:54:09.900][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-27 21:54:09.901][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-27 21:54:09.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:09.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:09.905][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:54:09.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:09.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:09.909][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:54:09.911][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:09.912][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:54:09.913][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:54:09.915][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:09.916][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:09.918][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-27 21:54:09.920][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:09.922][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-27 21:54:09.923][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:09.925][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:54:09.926][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:09.927][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-27 21:54:09.929][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:09.930][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:54:09.932][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-27 21:54:09.933][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:54:09.935][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:09.936][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-27 21:54:09.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:54:09.939][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:09.941][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:09.942][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-27 21:54:09.942][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-27 21:54:09.942][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-27 21:54:09.942][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-27 21:54:09.942][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-27 21:54:09.944][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-27 21:54:09.945][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:09.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:09.948][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:54:09.949][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:09.950][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:09.952][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:54:09.953][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:09.954][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:54:09.956][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:54:09.957][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:09.959][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:09.960][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-27 21:54:09.963][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:09.965][self$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[2023-02-27 21:54:09.966][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:09.967][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:54:09.969][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:09.970][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-27 21:54:09.971][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:09.973][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:54:09.974][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-27 21:54:09.976][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:54:09.977][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:09.979][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-27 21:54:09.980][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:54:09.981][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:09.983][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:09.992][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:09.994][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-27 21:54:09.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:09.997][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:09.998][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:54:10.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:10.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:10.003][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:54:10.004][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:10.005][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:54:10.007][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:54:10.008][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:10.009][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:10.011][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-27 21:54:10.013][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:10.015][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-27 21:54:10.016][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:10.018][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:54:10.019][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:10.020][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-27 21:54:10.022][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:10.023][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:54:10.024][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-27 21:54:10.026][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:54:10.027][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:10.029][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-27 21:54:10.030][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:54:10.031][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:10.033][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:10.034][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:10.036][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-27 21:54:10.037][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:10.038][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:10.040][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:54:10.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:10.042][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:10.043][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:54:10.045][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:10.046][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:54:10.047][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:54:10.049][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:10.050][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:10.052][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-27 21:54:10.053][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.073][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[2023-02-27 21:54:10.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.079][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[2023-02-27 21:54:10.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.105][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[2023-02-27 21:54:10.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.145][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[2023-02-27 21:54:10.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.151][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[2023-02-27 21:54:10.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.157][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[2023-02-27 21:54:10.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.163][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[2023-02-27 21:54:10.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.170][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[2023-02-27 21:54:10.171][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-27 21:54:10.173][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-27 21:54:10.175][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-27 21:54:10.177][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-27 21:54:10.179][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-27 21:54:10.181][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-27 21:54:10.183][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-27 21:54:10.185][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-27 21:54:10.187][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-27 21:54:10.189][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-27 21:54:10.191][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-27 21:54:10.193][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-27 21:54:10.195][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-27 21:54:10.197][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-27 21:54:10.199][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-27 21:54:10.201][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-27 21:54:10.203][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-27 21:54:10.206][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-27 21:54:10.208][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-27 21:54:10.210][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-27 21:54:10.211][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-27 21:54:10.213][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-27 21:54:10.215][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-27 21:54:10.217][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-27 21:54:10.219][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-27 21:54:10.221][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-27 21:54:10.223][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-27 21:54:10.225][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-27 21:54:10.227][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-27 21:54:10.229][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-27 21:54:10.231][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-27 21:54:10.233][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-27 21:54:10.235][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-27 21:54:10.237][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-27 21:54:10.239][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-27 21:54:10.241][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-27 21:54:10.243][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-27 21:54:10.245][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-27 21:54:10.247][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-27 21:54:10.249][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-27 21:54:10.251][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-27 21:54:10.253][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-27 21:54:10.255][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-27 21:54:10.257][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-27 21:54:10.259][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-27 21:54:10.261][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-27 21:54:10.263][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-27 21:54:10.265][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-27 21:54:10.267][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-27 21:54:10.269][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-27 21:54:10.271][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-27 21:54:10.273][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-27 21:54:10.275][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-27 21:54:10.277][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-27 21:54:10.279][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-27 21:54:10.281][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-27 21:54:10.283][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-27 21:54:10.294][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-27 21:54:10.296][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-27 21:54:10.298][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-27 21:54:10.300][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-27 21:54:10.302][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-27 21:54:10.304][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-27 21:54:10.306][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-27 21:54:10.308][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-27 21:54:10.310][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-27 21:54:10.312][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-27 21:54:10.315][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-27 21:54:10.317][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-27 21:54:10.319][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-27 21:54:10.321][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-27 21:54:10.323][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-27 21:54:10.325][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-27 21:54:10.327][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-27 21:54:10.329][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-27 21:54:10.331][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-27 21:54:10.333][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-27 21:54:10.335][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-27 21:54:10.337][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-27 21:54:10.339][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-27 21:54:10.341][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-27 21:54:10.343][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-27 21:54:10.345][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-27 21:54:10.347][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-27 21:54:10.349][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-27 21:54:10.351][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-27 21:54:10.352][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.355][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.365][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[2023-02-27 21:54:10.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.374][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[2023-02-27 21:54:10.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-27 21:54:10.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:10.518][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-02-27 21:54:10.520][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-02-27 21:54:10.523][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:10.524][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-27 21:54:10.526][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:10.527][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-27 21:54:10.528][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:10.530][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-02-27 21:54:10.531][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:10.533][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-27 21:54:10.534][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-27 21:54:10.535][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-27 21:54:10.537][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:10.538][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-02-27 21:54:10.540][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-02-27 21:54:10.541][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-02-27 21:54:10.543][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-27 21:54:10.544][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-27 21:54:10.544][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-02-27 21:54:10.545][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-27 21:54:10.547][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:10.548][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:10.549][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-27 21:54:10.551][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-27 21:54:10.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-27 21:54:10.553][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-27 21:54:10.555][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-02-27 21:54:10.555][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-02-27 21:54:10.556][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:54:10.557][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:54:10.559][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-27 21:54:10.560][self$setPropertyValue]
biodb.DEBUG[2023-02-27 21:54:10.562][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-27 21:54:10.564][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-27 21:54:10.566][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-27 21:54:10.568][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-27 21:54:10.573][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-02-27 21:54:10.574][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-02-27 21:54:10.576][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-02-27 21:54:10.578][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-27 21:54:10.580][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:54:10.581][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:54:10.583][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-02-27 21:54:10.584][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-02-27 21:54:10.586][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-02-27 21:54:10.586][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-02-27 21:54:10.587][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-27 21:54:10.596][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-27 21:54:10.598][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-02-27 21:54:10.599][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-02-27 21:54:10.601][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-02-27 21:54:10.603][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-27 21:54:10.605][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:54:10.606][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:54:10.608][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-27 21:54:10.610][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-27 21:54:10.611][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-02-27 21:54:10.613][biodb::testThat]
biodb.INFO [2023-02-27 21:54:10.615][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2023-02-27 21:54:10.616][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-27 21:54:10.617][biodb::testThat]
biodb.DEBUG[2023-02-27 21:54:10.631][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-02-27 21:54:10.632][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2023-02-27 21:54:10.633][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2023-02-27 21:54:10.638][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:10.640][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:10.642][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-27 21:54:10.644][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:10.645][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-27 21:54:10.651][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-27 21:54:10.652][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-27 21:54:10.653][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-27 21:54:10.655][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-27 21:54:10.656][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-02-27 21:54:10.658][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2023-02-27 21:54:10.660][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-02-27 21:54:10.661][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-02-27 21:54:10.664][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:10.666][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-02-27 21:54:10.668][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-02-27 21:54:10.670][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-27 21:54:10.673][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-02-27 21:54:10.675][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-02-27 21:54:10.695][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-27 21:54:10.697][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-27 21:54:10.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-27 21:54:10.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:10.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:10.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:10.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:10.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:10.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-27 21:54:10.719][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:10.720][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:10.722][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.723][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:10.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:10.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.734][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:10.736][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:10.737][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.738][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.740][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:10.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:10.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.759][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:10.760][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:10.762][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.763][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.765][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:10.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:10.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.774][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:10.776][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:10.777][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.778][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:10.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:10.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.790][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:10.791][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:10.793][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.794][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:10.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:10.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.805][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:10.807][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:10.809][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.811][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.813][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:10.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:10.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.822][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:10.824][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:10.825][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.827][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.829][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:10.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:10.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.838][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:10.840][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:10.841][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.843][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.845][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:10.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:10.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.854][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:10.855][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:10.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.858][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.860][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:10.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:10.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.869][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:10.871][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:10.872][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.874][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.875][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:10.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:10.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.889][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:10.891][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:10.893][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.895][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:10.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:10.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.908][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:10.910][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:10.911][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.913][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:10.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:10.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.950][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:10.952][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:10.953][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.955][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:10.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:10.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.967][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:10.968][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:10.970][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.971][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:10.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:10.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.983][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:10.984][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:10.986][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.987][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.989][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:10.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:10.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:10.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:10.999][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:11.000][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:11.002][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.003][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.005][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:11.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:11.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.016][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-02-27 21:54:11.018][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:11.019][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.020][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.022][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-02-27 21:54:11.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:11.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.050][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.056][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.062][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.068][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.074][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.079][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.128][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.134][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.140][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.146][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.151][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.157][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.163][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:11.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:11.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.169][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:11.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:11.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.174][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:11.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:11.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.180][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:11.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:11.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.185][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:11.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:11.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.191][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:11.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:11.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.197][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:11.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:11.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.202][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:11.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:11.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.208][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:11.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:11.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:11.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:11.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.221][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:11.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:11.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:11.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:11.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.232][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.243][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.249][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:11.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:11.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.254][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:11.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:11.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.260][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:11.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:11.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:11.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:11.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:11.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:11.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:11.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:11.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.292][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:11.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:11.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:11.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:11.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:11.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:11.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.308][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:11.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:11.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.314][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:11.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:11.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.320][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:11.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:11.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.325][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:11.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:11.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.331][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:11.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:11.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.336][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:11.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:11.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.342][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-27 21:54:11.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.353][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.364][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-27 21:54:11.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.375][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:11.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:11.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:11.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:11.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:11.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:11.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:11.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:11.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:11.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:11.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.407][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:11.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:11.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.413][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:11.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:11.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.435][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:11.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:11.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:11.478][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-02-27 21:54:11.480][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:11.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:11.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.486][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:11.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:11.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.491][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:11.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:11.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.497][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:11.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:11.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:11.503][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-27 21:54:11.504][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-02-27 21:54:11.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-27 21:54:11.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:11.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:11.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:11.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:11.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:11.519][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[2023-02-27 21:54:11.521][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-02-27 21:54:11.523][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-02-27 21:54:11.525][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:11.527][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-02-27 21:54:11.530][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-02-27 21:54:11.532][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-27 21:54:11.534][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-02-27 21:54:11.535][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-02-27 21:54:11.556][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-27 21:54:11.558][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-27 21:54:11.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-27 21:54:11.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:11.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:11.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:11.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:11.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:11.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-27 21:54:11.579][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.581][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.591][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.592][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.604][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.606][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.607][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.608][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.610][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.620][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.621][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.623][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.625][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.628][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.637][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.639][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.640][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.641][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.653][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.654][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.656][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.657][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.668][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:11.670][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:11.671][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.673][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.675][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:11.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:11.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.684][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:11.686][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:11.687][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.688][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.690][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:11.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:11.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.699][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.701][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.702][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.704][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.706][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.715][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.716][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.718][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.719][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.721][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.730][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:11.732][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:11.733][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.734][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.736][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:11.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:11.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.746][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:11.747][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:11.757][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.759][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.761][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:11.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:11.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.771][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.773][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.774][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.775][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:11.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.787][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:11.788][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:11.790][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.791][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:11.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:11.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.803][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:11.804][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:11.805][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.807][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:11.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:11.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.818][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:11.820][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:11.821][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.822][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.824][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:11.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:11.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.835][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:11.837][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:11.838][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.839][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.841][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:11.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:11.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.851][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-02-27 21:54:11.852][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:11.854][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.855][ef$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.857][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-02-27 21:54:11.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:11.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:11.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:11.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.883][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.889][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.895][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-27 21:54:11.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.900][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.906][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.911][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-27 21:54:11.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-27 21:54:11.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-27 21:54:11.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.960][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.966][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.972][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-27 21:54:11.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.977][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.983][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.989][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-27 21:54:11.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:11.994][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:11.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:11.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:11.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.000][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:12.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:12.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.006][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:12.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-27 21:54:12.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.012][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.017][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.023][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.028][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:12.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:12.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.036][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:12.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:12.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.042][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-27 21:54:12.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-27 21:54:12.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.047][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:12.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:12.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:12.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:12.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-27 21:54:12.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-27 21:54:12.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.084][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.090][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:12.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:12.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.096][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:12.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:12.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.101][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:12.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-27 21:54:12.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:12.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:12.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:12.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:12.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:12.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-27 21:54:12.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.123][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:12.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:12.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.128][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:12.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:12.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.134][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:12.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:12.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.139][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:12.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:12.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.145][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:12.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:12.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.150][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:12.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-27 21:54:12.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.156][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:12.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:12.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.161][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:12.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:12.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.167][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-27 21:54:12.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-27 21:54:12.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.172][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-27 21:54:12.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.178][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.183][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.189][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.194][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-27 21:54:12.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-27 21:54:12.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.205][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:12.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:12.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.210][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:12.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:12.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.216][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:12.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:12.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:12.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:12.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-27 21:54:12.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-27 21:54:12.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.248][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:12.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:12.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.254][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:12.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:12.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:12.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:12.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.265][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:12.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-27 21:54:12.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:12.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:12.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:12.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:12.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:12.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:12.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:12.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:12.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:12.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:12.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-27 21:54:12.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-27 21:54:12.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:12.308][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-02-27 21:54:12.310][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.315][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.321][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.327][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:12.332][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-27 21:54:12.334][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2023-02-27 21:54:12.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-27 21:54:12.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:12.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:12.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:12.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:12.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:12.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:12.365][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-02-27 21:54:12.366][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-02-27 21:54:12.368][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-02-27 21:54:12.370][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:12.372][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:12.374][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-27 21:54:12.376][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:12.377][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-27 21:54:12.383][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-27 21:54:12.384][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-27 21:54:12.385][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-27 21:54:12.387][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-27 21:54:12.396][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-02-27 21:54:12.398][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-02-27 21:54:12.401][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.407][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.412][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.418][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.424][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.429][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.435][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:12.442][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-27 21:54:12.443][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-02-27 21:54:12.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-27 21:54:12.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:12.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:12.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:12.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:12.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:12.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-27 21:54:12.460][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.466][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.471][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.477][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.482][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.488][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.493][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:12.499][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-02-27 21:54:12.500][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-02-27 21:54:12.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-27 21:54:12.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:12.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:12.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:12.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:12.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:12.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-27 21:54:12.530][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-02-27 21:54:12.532][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-02-27 21:54:12.533][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-02-27 21:54:12.535][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:12.537][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:12.539][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-27 21:54:12.541][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-27 21:54:12.542][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-27 21:54:12.557][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-27 21:54:12.558][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-27 21:54:12.560][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-27 21:54:12.561][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-27 21:54:12.563][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-02-27 21:54:12.564][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-02-27 21:54:12.567][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.572][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.578][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.583][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.589][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.594][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.599][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:12.605][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-02-27 21:54:12.606][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2023-02-27 21:54:12.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-27 21:54:12.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:12.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:12.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:12.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:12.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:12.621][FUN] Functions in observer BiodbConfig: [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[2023-02-27 21:54:12.623][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.628][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.634][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.639][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.646][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.652][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-27 21:54:12.657][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-27 21:54:12.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-27 21:54:12.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-27 21:54:12.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-27 21:54:12.663][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-27 21:54:12.664][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-02-27 21:54:12.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-27 21:54:12.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:12.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:12.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:12.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:12.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:12.679][FUN] Functions in observer BiodbConfig: [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 [2023-02-27 21:54:12.684][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-27 21:54:12.685][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-02-27 21:54:12.687][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-02-27 21:54:12.688][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-27 21:54:12.689][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-27 21:54:12.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-27 21:54:12.692][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-27 21:54:12.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-27 21:54:12.694][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-27 21:54:12.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 186 ]
>
> proc.time()
user system elapsed
12.696 0.545 18.114
biodbHmdb.Rcheck/biodbHmdb-Ex.timings
| name | user | system | elapsed | |
| HmdbMetabolitesConn | 2.199 | 0.194 | 2.394 | |
| HmdbMetabolitesEntry | 0.444 | 0.004 | 0.447 | |