| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:14:53 -0000 (Wed, 08 Feb 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" | 4164 |
| 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 181/2164 | 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: 2023-02-06 19:00:18 -0000 (Mon, 06 Feb 2023) |
| EndedAt: 2023-02-06 19:01:39 -0000 (Mon, 06 Feb 2023) |
| EllapsedTime: 81.1 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 [2023-02-06 19:01:11.898][biodb::testContext]
biodb.INFO [2023-02-06 19:01:11.900][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:01:11.902][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2023-02-06 19:01:11.903][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:01:11.904][biodb::testContext]
biodb.INFO [2023-02-06 19:01:11.906][biodb::testThat]
biodb.INFO [2023-02-06 19:01:11.908][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2023-02-06 19:01:11.909][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:11.910][biodb::testThat]
biodb.INFO [2023-02-06 19:01:12.088][biodb::testContext]
biodb.INFO [2023-02-06 19:01:12.089][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:01:12.091][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-02-06 19:01:12.092][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:01:12.094][biodb::testContext]
biodb.INFO [2023-02-06 19:01:12.116][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:01:12.119][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-06 19:01:12.129][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:01:12.130][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-06 19:01:12.132][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-06 19:01:12.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.138][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-06 19:01:12.164][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-06 19:01:12.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.170][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-06 19:01:12.171][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-06 19:01:12.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.176][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-06 19:01:12.178][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-06 19:01:12.179][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-06 19:01:12.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.184][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-06 19:01:12.186][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-06 19:01:12.187][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-06 19:01:12.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.192][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-06 19:01:12.194][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-06 19:01:12.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.197][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[2023-02-06 19:01:12.199][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-06 19:01:12.200][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-06 19:01:12.202][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-06 19:01:12.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.207][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-06 19:01:12.208][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-06 19:01:12.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.213][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-06 19:01:12.215][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-06 19:01:12.216][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-06 19:01:12.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.221][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:01:12.223][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-06 19:01:12.224][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-06 19:01:12.236][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-06 19:01:12.238][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-06 19:01:12.239][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-06 19:01:12.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.244][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-06 19:01:12.246][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-06 19:01:12.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.251][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-06 19:01:12.253][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-06 19:01:12.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.258][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-06 19:01:12.259][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-06 19:01:12.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.264][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-06 19:01:12.266][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-06 19:01:12.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.270][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[2023-02-06 19:01:12.271][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-06 19:01:12.273][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-06 19:01:12.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.278][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:01:12.279][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-06 19:01:12.284][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-06 19:01:12.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.288][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[2023-02-06 19:01:12.289][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-06 19:01:12.291][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-06 19:01:12.292][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-06 19:01:12.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.301][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-06 19:01:12.349][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:12.372][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-02-06 19:01:12.373][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.375][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:12.376][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.378][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:12.379][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:12.380][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:12.382][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:01:12.383][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:12.385][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.386][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-06 19:01:12.388][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:12.389][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.390][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.392][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:01:12.392][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:01:12.392][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:01:12.392][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:01:12.392][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:01:12.393][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:12.395][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:12.396][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:12.397][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:12.399][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:12.400][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:12.401][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:12.403][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.404][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:12.405][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:12.407][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:12.408][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.410][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-06 19:01:12.412][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:12.414][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:01:12.415][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.417][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:12.418][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.420][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:12.421][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:12.422][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:12.424][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:01:12.425][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:12.427][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.429][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-06 19:01:12.430][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:12.431][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.433][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.434][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:01:12.434][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:01:12.434][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:01:12.434][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:01:12.434][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:01:12.436][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:12.437][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:12.438][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:12.440][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:12.441][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:12.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:12.444][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:12.446][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.447][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:12.449][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:12.450][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:12.452][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.454][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-06 19:01:12.456][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.458][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-02-06 19:01:12.460][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.461][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:12.463][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.464][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:12.466][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:12.468][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:12.469][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:01:12.471][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:12.472][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:12.474][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-06 19:01:12.475][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:12.477][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.479][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.480][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.490][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:12.492][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:12.494][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:12.495][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:12.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:12.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:12.500][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:12.501][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.503][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:12.504][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:12.506][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:12.507][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.509][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-06 19:01:12.512][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.513][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:01:12.515][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.516][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:12.518][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.519][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:12.521][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:12.522][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:12.524][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:01:12.525][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:12.527][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:12.528][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-06 19:01:12.530][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:12.531][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.533][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:12.534][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.536][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:12.537][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:12.539][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:12.540][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:12.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:12.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:12.544][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:12.546][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.547][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:12.548][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:12.550][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:12.551][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:12.557][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:01:12.558][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.673][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-06 19:01:12.680][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-06 19:01:12.682][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-06 19:01:12.684][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-06 19:01:12.686][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:01:12.689][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-06 19:01:12.691][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-06 19:01:12.693][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-06 19:01:12.695][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-06 19:01:12.697][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-06 19:01:12.699][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:01:12.701][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-06 19:01:12.703][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-06 19:01:12.705][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-06 19:01:12.707][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-06 19:01:12.709][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:01:12.711][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-06 19:01:12.714][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-06 19:01:12.716][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:01:12.718][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-06 19:01:12.720][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-06 19:01:12.722][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-06 19:01:12.724][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-06 19:01:12.726][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-06 19:01:12.728][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-06 19:01:12.730][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-06 19:01:12.732][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-06 19:01:12.734][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-06 19:01:12.736][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-06 19:01:12.738][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-06 19:01:12.741][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-06 19:01:12.743][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-06 19:01:12.753][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-06 19:01:12.755][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-06 19:01:12.757][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-06 19:01:12.759][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-06 19:01:12.761][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-06 19:01:12.763][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-06 19:01:12.765][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-06 19:01:12.767][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-06 19:01:12.769][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-06 19:01:12.772][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-06 19:01:12.774][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-06 19:01:12.776][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-06 19:01:12.778][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-06 19:01:12.780][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-06 19:01:12.782][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-06 19:01:12.784][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-06 19:01:12.786][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-06 19:01:12.788][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-06 19:01:12.790][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-06 19:01:12.792][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-06 19:01:12.794][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-06 19:01:12.796][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-06 19:01:12.798][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-06 19:01:12.801][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-06 19:01:12.803][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-06 19:01:12.805][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-06 19:01:12.807][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-06 19:01:12.809][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-06 19:01:12.811][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-06 19:01:12.813][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-06 19:01:12.815][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-06 19:01:12.817][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-06 19:01:12.820][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-06 19:01:12.822][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-06 19:01:12.824][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:01:12.826][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:01:12.828][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-06 19:01:12.830][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-06 19:01:12.833][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-06 19:01:12.835][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-06 19:01:12.837][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-06 19:01:12.839][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-06 19:01:12.841][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-06 19:01:12.843][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-06 19:01:12.845][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-06 19:01:12.847][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-06 19:01:12.849][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-06 19:01:12.852][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-06 19:01:12.854][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-06 19:01:12.856][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-06 19:01:12.858][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-06 19:01:12.866][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-06 19:01:12.869][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:01:12.873][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:01:12.875][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.877][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.902][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[2023-02-06 19:01:12.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:12.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:12.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:12.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:12.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:12.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:12.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:12.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:13.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:13.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:13.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:13.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:13.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:13.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:13.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:13.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:13.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:13.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:13.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:13.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:13.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:13.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:13.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:13.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:13.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:13.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:13.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:13.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:13.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:13.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:13.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:13.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:13.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:13.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:13.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:13.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:13.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:13.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:13.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:13.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:13.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:13.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:13.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:13.074][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[2023-02-06 19:01:13.076][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-02-06 19:01:13.089][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-02-06 19:01:13.092][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:13.093][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-06 19:01:13.095][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:13.096][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:13.098][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:13.099][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-02-06 19:01:13.100][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:13.102][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:13.103][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-06 19:01:13.105][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:13.106][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:13.107][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-02-06 19:01:13.109][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-02-06 19:01:13.110][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-02-06 19:01:13.112][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:13.113][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:01:13.113][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-02-06 19:01:13.115][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-06 19:01:13.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:13.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:13.119][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:13.120][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:13.121][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:13.122][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:13.124][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-02-06 19:01:13.124][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-02-06 19:01:13.125][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:13.126][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:13.128][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:13.129][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:13.138][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-06 19:01:13.140][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-06 19:01:13.142][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:01:13.144][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:01:13.175][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-02-06 19:01:13.177][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-02-06 19:01:13.183][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-02-06 19:01:13.188][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-06 19:01:13.194][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:13.196][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:13.198][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-02-06 19:01:13.199][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-02-06 19:01:13.200][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-02-06 19:01:13.200][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-02-06 19:01:13.202][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:13.203][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:13.204][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-02-06 19:01:13.206][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-02-06 19:01:13.207][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-02-06 19:01:13.231][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-06 19:01:13.233][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:13.234][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:13.236][private$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[2023-02-06 19:01:13.238][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:13.239][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-02-06 19:01:13.259][biodb::testThat]
biodb.INFO [2023-02-06 19:01:13.261][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-02-06 19:01:13.262][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:13.264][biodb::testThat]
biodb.TRACE[2023-02-06 19:01:13.270][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[2023-02-06 19:01:13.288][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:13.293][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-06 19:01:13.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:13.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:13.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:13.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:13.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:13.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:13.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:13.334][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:13.335][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:13.337][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.338][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:13.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:13.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.366][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:13.368][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:13.369][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.371][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.408][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:13.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:13.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.417][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:13.419][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:13.420][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.422][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.424][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:13.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:13.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.433][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:13.435][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:13.436][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.438][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:13.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:13.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.449][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:13.451][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:13.452][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.453][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:13.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:13.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.465][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:13.466][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:13.468][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.469][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.471][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:13.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:13.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.481][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:13.482][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:13.484][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.485][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.487][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:13.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:13.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.497][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:13.508][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:13.510][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.511][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.513][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:13.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:13.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.523][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:13.524][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:13.526][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.527][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.529][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:13.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:13.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.539][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:13.540][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:13.542][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.543][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.545][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:13.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:13.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.554][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:13.556][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:13.557][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.559][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.561][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:13.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:13.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.571][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:13.572][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:13.574][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.575][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:13.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:13.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.587][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:13.588][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:13.590][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.591][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:13.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:13.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.603][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:13.605][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:13.606][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.607][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.609][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:13.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:13.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.619][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:13.620][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:13.622][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.623][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.625][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:13.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:13.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.634][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:13.636][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:13.637][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.639][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.641][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:13.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:13.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.650][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-02-06 19:01:13.652][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:13.653][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.655][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.657][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-02-06 19:01:13.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:13.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:13.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:13.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:13.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:13.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:13.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:13.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.737][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:13.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:13.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.743][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:13.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:13.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.748][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:13.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:13.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.754][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:13.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:13.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.759][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:13.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:13.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.765][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:13.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:13.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:13.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:13.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:13.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:13.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:13.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:13.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:13.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:13.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:13.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:13.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:13.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:13.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.804][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:13.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:13.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.809][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:13.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:13.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.814][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:13.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:13.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.820][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:13.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:13.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.825][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:13.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:13.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.831][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:13.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:13.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.836][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:13.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:13.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.842][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:13.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:13.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.847][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:13.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:13.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.853][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:13.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:13.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.858][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:13.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:13.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.864][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:13.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:13.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.869][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:13.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:13.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.875][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:13.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:13.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.880][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:13.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:13.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:13.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:13.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.891][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:13.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:13.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:13.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:13.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:13.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:13.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:13.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:13.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.921][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:13.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:13.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.927][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:13.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:13.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.932][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:13.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:13.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.938][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:13.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:13.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:13.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:13.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:13.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:13.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:13.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:13.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:13.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:13.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:13.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:13.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.972][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:13.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:13.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.977][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:13.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:13.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.983][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:13.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:13.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.989][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:13.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:13.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:13.994][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:13.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:13.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:13.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.000][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:14.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:14.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.006][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:14.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:14.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.011][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-06 19:01:14.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.017][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.035][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-06 19:01:14.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.071][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:14.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:14.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.077][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:14.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:14.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:14.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:14.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:14.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:14.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.095][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:14.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:14.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.113][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.120][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.132][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:14.177][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2023-02-06 19:01:14.185][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:01:14.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:01:14.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.190][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:01:14.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:01:14.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.196][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-06 19:01:14.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-06 19:01:14.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.202][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-06 19:01:14.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-06 19:01:14.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.240][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.290][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.296][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.302][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:14.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.345][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.347][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.348][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.350][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:14.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:14.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:14.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:14.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:14.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:14.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:14.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:14.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.385][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:14.387][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:14.388][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.390][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:14.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:14.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.407][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:14.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:14.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.413][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:14.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:14.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.419][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:14.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:14.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.425][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:14.426][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:14.428][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.429][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.430][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:14.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:14.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.464][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.466][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.467][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.468][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:14.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.486][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:14.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:14.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.492][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:14.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:14.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.497][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:14.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:14.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.503][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:14.505][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:14.506][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.507][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.509][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:14.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:14.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:14.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:14.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:14.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:14.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:14.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:14.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.550][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:14.551][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:14.552][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.554][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:14.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:14.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.571][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:14.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:14.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.577][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:14.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:14.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.583][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:14.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:14.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.588][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:14.590][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:14.591][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.593][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.594][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:14.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:14.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.610][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:14.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:14.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.615][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:14.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:14.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.621][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:14.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:14.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.627][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:14.628][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:14.630][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.631][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.633][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:14.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:14.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.648][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:14.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:14.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.654][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:14.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:14.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.660][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:14.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:14.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.666][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:14.667][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:14.669][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.670][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.671][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:14.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:14.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:14.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:14.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:14.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:14.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:14.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:14.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.705][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:14.706][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:14.708][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.709][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:14.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:14.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.726][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:14.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:14.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.740][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:14.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:14.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.746][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:14.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:14.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.751][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:14.753][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:14.754][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.756][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.757][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:14.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:14.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.773][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:14.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:14.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.779][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:14.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:14.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.785][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:14.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:14.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.791][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:14.793][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:14.794][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.795][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.797][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:14.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:14.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.813][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:14.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:14.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.820][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:14.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:14.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.826][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:14.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:14.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.832][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:14.833][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:14.835][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.836][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.837][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:14.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:14.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.854][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:14.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:14.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.860][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:14.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:14.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.866][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:14.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:14.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.871][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:14.873][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:14.874][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.875][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.877][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:14.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:14.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:14.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:14.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:14.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:14.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:14.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:14.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.910][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:14.911][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:14.913][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.914][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:14.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:14.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.931][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.944][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.956][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.958][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.959][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.961][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.962][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:14.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.978][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:14.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:14.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.985][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:14.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:14.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.991][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:14.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:14.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:14.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:14.997][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:14.998][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.000][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.001][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.003][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.019][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:15.021][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:15.022][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.024][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.032][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:15.034][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:15.035][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.037][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.045][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.047][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.048][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.049][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.058][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:15.059][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:15.061][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.062][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.070][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:15.072][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:15.073][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.075][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.083][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:15.085][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:15.086][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.088][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.096][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:15.097][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:15.099][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.100][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.108][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:15.110][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:15.112][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.113][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.121][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:15.123][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:15.124][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.126][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.134][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:15.135][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:15.137][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.138][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.154][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:15.156][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:15.157][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.159][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.167][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:15.169][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:15.170][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.172][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.180][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:15.182][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:15.183][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.185][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.193][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:15.195][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:15.197][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.198][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.206][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:15.208][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:15.209][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.211][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.219][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:15.220][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:15.222][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.223][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.231][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:15.233][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:15.234][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.236][ef$get] fields variable is a list.
biodb.INFO [2023-02-06 19:01:15.245][biodb::testThat]
biodb.INFO [2023-02-06 19:01:15.246][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-02-06 19:01:15.248][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:15.249][biodb::testThat]
biodb.DEBUG[2023-02-06 19:01:15.269][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-02-06 19:01:15.280][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-02-06 19:01:15.287][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:15.289][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-02-06 19:01:15.292][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-02-06 19:01:15.294][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:01:15.298][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-02-06 19:01:15.300][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:15.366][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:15.368][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-06 19:01:15.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:15.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:15.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:15.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:15.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:15.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:15.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:15.391][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:15.393][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:15.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.396][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:15.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:15.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.408][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:15.410][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:15.411][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.413][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.415][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:15.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:15.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.425][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.427][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.428][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.430][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.432][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.442][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:15.444][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:15.446][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.447][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:15.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:15.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.459][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:15.461][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:15.462][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.464][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:15.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:15.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.476][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:15.478][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:15.479][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.481][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.483][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:15.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:15.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.493][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:15.495][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:15.496][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.498][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.500][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:15.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:15.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.510][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:15.512][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:15.514][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.515][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.517][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:15.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:15.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.528][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:15.529][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:15.531][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.532][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.534][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:15.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:15.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.544][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:15.546][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:15.548][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.549][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.551][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:15.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:15.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.568][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:15.570][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:15.572][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.573][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:15.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:15.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.585][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:15.586][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:15.588][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.589][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.591][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:15.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:15.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.601][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:15.603][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:15.604][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.606][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:15.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:15.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.618][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:15.620][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:15.621][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.622][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:15.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:15.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.634][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:15.636][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:15.637][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.639][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.640][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:15.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:15.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.650][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:15.652][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:15.654][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.655][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.657][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:15.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:15.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.667][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-02-06 19:01:15.669][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:15.670][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.672][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.674][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-02-06 19:01:15.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:15.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:15.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:15.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:15.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:15.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:15.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:15.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.702][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:15.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:15.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.708][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:15.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:15.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.714][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:15.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:15.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.721][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.727][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.733][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:15.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:15.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:15.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:15.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:15.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:15.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:15.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:15.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:15.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:15.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:15.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:15.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:15.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.787][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:15.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:15.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.793][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:15.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:15.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.800][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:15.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:15.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.806][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:15.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:15.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.813][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:15.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:15.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.819][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:15.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:15.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.826][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:15.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:15.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.832][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:15.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:15.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.839][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:15.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:15.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.845][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:15.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:15.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.851][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:15.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:15.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.857][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:15.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:15.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.863][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:15.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:15.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.869][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:15.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:15.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.875][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:15.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:15.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:15.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:15.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.887][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:15.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:15.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:15.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:15.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:15.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:15.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:15.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:15.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.911][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:15.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:15.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.917][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:15.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:15.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.923][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:15.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:15.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.929][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:15.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:15.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:15.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:15.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:15.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:15.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:15.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:15.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.953][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:15.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:15.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:15.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:15.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:15.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:15.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.970][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:15.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:15.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.983][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:15.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:15.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.989][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:15.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:15.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:15.995][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:15.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:15.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:15.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.001][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:16.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:16.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.007][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:16.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:16.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.012][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-06 19:01:16.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:16.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:16.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:16.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:16.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:16.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:16.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:16.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.036][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-06 19:01:16.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:16.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.058][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.070][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.079][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:16.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:16.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.085][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:16.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:16.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.097][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:16.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:16.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:16.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:16.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:16.141][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-02-06 19:01:16.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-02-06 19:01:16.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-02-06 19:01:16.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-02-06 19:01:16.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-02-06 19:01:16.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-02-06 19:01:16.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-02-06 19:01:16.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:01:16.166][biodb::testThat]
biodb.INFO [2023-02-06 19:01:16.168][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-02-06 19:01:16.177][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:16.178][biodb::testThat]
biodb.TRACE[2023-02-06 19:01:16.182][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.183][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.185][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.186][ef$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:16.188][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2023-02-06 19:01:16.228][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.233][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:16.247][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2023-02-06 19:01:16.259][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-02-06 19:01:16.261][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-02-06 19:01:16.262][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-02-06 19:01:16.264][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:16.266][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:16.268][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-06 19:01:16.270][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:16.272][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-06 19:01:16.277][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-06 19:01:16.279][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-06 19:01:16.281][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-06 19:01:16.282][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-06 19:01:16.283][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-02-06 19:01:16.285][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-02-06 19:01:16.287][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.293][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.299][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.305][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:16.311][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-06 19:01:16.312][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-02-06 19:01:16.313][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2023-02-06 19:01:16.333][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:16.335][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:16.336][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.338][ef$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:16.339][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2023-02-06 19:01:16.369][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:16.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:16.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.375][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:16.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:16.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.380][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:16.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:16.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:16.388][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[2023-02-06 19:01:16.476][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-02-06 19:01:16.477][private$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[2023-02-06 19:01:16.479][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2023-02-06 19:01:16.499][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:16.501][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:16.503][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-06 19:01:16.505][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:16.506][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-06 19:01:16.541][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-06 19:01:16.542][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-06 19:01:16.544][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-06 19:01:16.545][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-06 19:01:16.546][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-02-06 19:01:16.547][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-02-06 19:01:16.550][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:16.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:16.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.555][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:16.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:16.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.561][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:16.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:16.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.566][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:16.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:16.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:16.572][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-06 19:01:16.573][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-02-06 19:01:16.574][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2023-02-06 19:01:16.595][biodb::testThat]
biodb.INFO [2023-02-06 19:01:16.597][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-02-06 19:01:16.598][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:16.599][biodb::testThat]
biodb.TRACE[2023-02-06 19:01:16.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.629][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:16.663][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-02-06 19:01:16.664][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-02-06 19:01:16.666][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-02-06 19:01:16.668][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:16.670][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:16.672][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-06 19:01:16.674][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:16.675][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-06 19:01:16.681][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-06 19:01:16.682][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-06 19:01:16.683][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-06 19:01:16.685][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-06 19:01:16.686][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-02-06 19:01:16.688][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-02-06 19:01:16.690][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:16.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:16.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:16.720][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-06 19:01:16.722][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2023-02-06 19:01:16.743][biodb::testThat]
biodb.INFO [2023-02-06 19:01:16.745][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-02-06 19:01:16.746][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:16.747][biodb::testThat]
biodb.TRACE[2023-02-06 19:01:16.783][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:01:16.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:01:16.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.788][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:01:16.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:01:16.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.794][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-06 19:01:16.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-06 19:01:16.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.799][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-06 19:01:16.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-06 19:01:16.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.866][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:01:16.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:01:16.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.880][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:01:16.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:01:16.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.886][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-06 19:01:16.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-06 19:01:16.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:16.891][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-06 19:01:16.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-06 19:01:16.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:16.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:01:16.901][biodb::testThat]
biodb.INFO [2023-02-06 19:01:16.902][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-02-06 19:01:16.903][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:16.905][biodb::testThat]
biodb.INFO [2023-02-06 19:01:16.911][biodb::testThat]
biodb.INFO [2023-02-06 19:01:16.913][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-02-06 19:01:16.914][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:16.915][biodb::testThat]
biodb.INFO [2023-02-06 19:01:16.922][biodb::testThat]
biodb.INFO [2023-02-06 19:01:16.923][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-02-06 19:01:16.925][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:16.926][biodb::testThat]
biodb.DEBUG[2023-02-06 19:01:16.930][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2023-02-06 19:01:19.200][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2023-02-06 19:01:19.688][biodb::testThat]
biodb.INFO [2023-02-06 19:01:19.689][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-02-06 19:01:19.690][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:19.692][biodb::testThat]
biodb.DEBUG[2023-02-06 19:01:21.351][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2023-02-06 19:01:21.867][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:21.868][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:21.870][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:21.871][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:21.873][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:21.874][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:21.888][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:21.889][ef$get] fields variable is a list.
biodb.INFO [2023-02-06 19:01:21.891][biodb::testThat]
biodb.INFO [2023-02-06 19:01:21.892][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-02-06 19:01:21.894][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:21.895][biodb::testThat]
biodb.DEBUG[2023-02-06 19:01:21.898][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-02-06 19:01:22.012][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-02-06 19:01:22.014][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:22.016][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-02-06 19:01:22.040][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-02-06 19:01:22.042][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:22.044][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:22.045][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:22.047][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:22.068][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:22.070][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-06 19:01:22.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:22.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:22.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:22.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.086][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.TRACE[2023-02-06 19:01:22.089][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:22.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:22.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.094][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:22.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:22.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:22.146][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-02-06 19:01:22.147][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-02-06 19:01:22.169][biodb::testThat]
biodb.INFO [2023-02-06 19:01:22.170][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-02-06 19:01:22.172][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:22.173][biodb::testThat]
biodb.DEBUG[2023-02-06 19:01:22.182][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2023-02-06 19:01:22.184][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2023-02-06 19:01:22.185][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-02-06 19:01:22.188][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:22.190][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-02-06 19:01:22.193][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2023-02-06 19:01:22.194][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:01:22.196][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:01:22.198][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:22.200][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:22.222][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:22.224][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-06 19:01:22.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:22.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:22.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:22.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:22.242][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:22.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:22.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.248][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:22.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:22.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:22.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:22.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:22.295][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-02-06 19:01:22.296][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-02-06 19:01:22.297][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2023-02-06 19:01:22.313][biodb::testThat]
biodb.INFO [2023-02-06 19:01:22.315][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-02-06 19:01:22.316][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:22.318][biodb::testThat]
biodb.INFO [2023-02-06 19:01:22.345][biodb::testThat]
biodb.INFO [2023-02-06 19:01:22.346][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-02-06 19:01:22.347][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:22.349][biodb::testThat]
biodb.DEBUG[2023-02-06 19:01:22.352][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:22.354][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:22.356][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-06 19:01:22.358][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:22.359][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-06 19:01:22.365][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-06 19:01:22.366][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-06 19:01:22.368][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-06 19:01:22.369][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2023-02-06 19:01:22.377][biodb::testThat]
biodb.INFO [2023-02-06 19:01:22.379][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-02-06 19:01:22.380][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:22.381][biodb::testThat]
biodb.DEBUG[2023-02-06 19:01:22.385][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:22.388][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:22.390][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-06 19:01:22.391][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:22.393][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-06 19:01:22.398][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-06 19:01:22.400][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-06 19:01:22.401][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-06 19:01:22.402][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2023-02-06 19:01:22.428][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:22.429][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:22.431][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.432][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:22.433][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:22.434][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:22.436][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:22.437][ef$get] fields variable is a list.
biodb.INFO [2023-02-06 19:01:22.438][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-06 19:01:22.440][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-02-06 19:01:22.451][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-02-06 19:01:22.452][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-06 19:01:22.454][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:22.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:22.456][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.458][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.459][FUN] Functions in observer BiodbConfig: [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 [2023-02-06 19:01:22.464][biodb::testContext]
biodb.INFO [2023-02-06 19:01:22.466][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:01:22.467][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2023-02-06 19:01:22.468][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:01:22.470][biodb::testContext]
biodb.INFO [2023-02-06 19:01:22.477][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:01:22.479][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-06 19:01:22.484][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:01:22.485][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-06 19:01:22.487][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-06 19:01:22.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.492][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-06 19:01:22.493][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-06 19:01:22.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.498][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-06 19:01:22.500][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-06 19:01:22.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.505][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-06 19:01:22.506][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-06 19:01:22.508][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-06 19:01:22.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.513][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-06 19:01:22.514][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-06 19:01:22.516][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-06 19:01:22.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.521][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-06 19:01:22.522][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-06 19:01:22.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.527][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-06 19:01:22.529][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-06 19:01:22.530][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-06 19:01:22.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.535][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-06 19:01:22.537][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-06 19:01:22.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.542][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-06 19:01:22.543][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-06 19:01:22.545][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-06 19:01:22.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.550][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:01:22.551][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-06 19:01:22.553][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-06 19:01:22.554][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-06 19:01:22.555][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-06 19:01:22.557][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-06 19:01:22.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.571][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-06 19:01:22.572][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-06 19:01:22.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.578][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-06 19:01:22.579][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-06 19:01:22.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.584][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-06 19:01:22.586][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-06 19:01:22.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.591][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-06 19:01:22.592][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-06 19:01:22.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.597][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-06 19:01:22.598][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-06 19:01:22.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.603][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:01:22.605][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-06 19:01:22.609][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-06 19:01:22.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.614][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-06 19:01:22.616][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-06 19:01:22.617][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-06 19:01:22.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.622][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-06 19:01:22.625][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:22.626][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-02-06 19:01:22.628][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.629][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:22.630][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.632][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:22.633][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:22.634][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:22.636][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:01:22.637][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:22.638][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.640][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-06 19:01:22.641][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:22.643][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.644][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.645][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:01:22.645][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:01:22.645][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:01:22.645][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:01:22.645][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:01:22.647][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:22.648][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:22.649][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:22.651][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:22.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:22.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:22.654][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:22.656][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.657][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:22.658][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:22.660][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:22.661][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.663][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-06 19:01:22.665][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:22.666][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:01:22.668][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.669][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:22.670][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.672][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:22.673][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:22.675][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:22.676][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:01:22.677][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:22.679][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.680][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-06 19:01:22.681][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:22.683][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.684][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.685][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:01:22.685][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:01:22.685][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:01:22.685][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:01:22.685][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:01:22.687][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:22.688][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:22.689][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:22.691][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:22.692][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:22.693][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:22.694][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:22.696][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.697][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:22.698][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:22.700][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:22.701][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.703][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-06 19:01:22.705][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.707][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-02-06 19:01:22.708][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.709][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:22.711][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.721][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:22.722][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:22.724][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:22.725][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:01:22.726][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:22.728][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:22.729][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-06 19:01:22.730][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:22.732][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.733][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.734][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.736][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:22.737][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:22.738][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:22.740][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:22.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:22.742][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:22.743][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:22.745][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.746][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:22.747][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:22.748][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:22.750][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.751][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-06 19:01:22.754][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.755][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:01:22.757][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.758][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:22.760][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.761][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:22.762][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:22.763][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:22.765][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:01:22.766][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:22.767][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:22.769][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-06 19:01:22.770][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:22.771][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.773][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:22.774][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.775][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:22.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:22.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:22.779][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:22.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:22.782][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:22.783][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:22.785][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.786][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:22.787][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:22.789][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:22.790][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:22.792][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:01:22.793][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.801][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[2023-02-06 19:01:22.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.813][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[2023-02-06 19:01:22.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.855][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[2023-02-06 19:01:22.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:22.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:22.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:22.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:22.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:22.906][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-06 19:01:22.908][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-06 19:01:22.909][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-06 19:01:22.911][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-06 19:01:22.913][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:01:22.915][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-06 19:01:22.917][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-06 19:01:22.918][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-06 19:01:22.920][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-06 19:01:22.922][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-06 19:01:22.924][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:01:22.926][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-06 19:01:22.928][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-06 19:01:22.929][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-06 19:01:22.931][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-06 19:01:22.933][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:01:22.935][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-06 19:01:22.937][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-06 19:01:22.939][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:01:22.940][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-06 19:01:22.942][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-06 19:01:22.944][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-06 19:01:22.946][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-06 19:01:22.948][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-06 19:01:22.950][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-06 19:01:22.951][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-06 19:01:22.953][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-06 19:01:22.955][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-06 19:01:22.957][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-06 19:01:22.959][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-06 19:01:22.961][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-06 19:01:22.962][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-06 19:01:22.964][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-06 19:01:22.966][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-06 19:01:22.968][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-06 19:01:22.970][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-06 19:01:22.972][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-06 19:01:22.974][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-06 19:01:22.976][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-06 19:01:22.978][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-06 19:01:22.980][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-06 19:01:22.982][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-06 19:01:22.984][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-06 19:01:22.986][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-06 19:01:22.988][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-06 19:01:22.990][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-06 19:01:22.992][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-06 19:01:22.994][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-06 19:01:23.004][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-06 19:01:23.006][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-06 19:01:23.008][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-06 19:01:23.010][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-06 19:01:23.012][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-06 19:01:23.014][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-06 19:01:23.016][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-06 19:01:23.018][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-06 19:01:23.020][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-06 19:01:23.022][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-06 19:01:23.024][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-06 19:01:23.026][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-06 19:01:23.028][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-06 19:01:23.029][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-06 19:01:23.031][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-06 19:01:23.033][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-06 19:01:23.035][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-06 19:01:23.037][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-06 19:01:23.039][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:01:23.041][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:01:23.043][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-06 19:01:23.045][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-06 19:01:23.047][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-06 19:01:23.049][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-06 19:01:23.051][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-06 19:01:23.052][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-06 19:01:23.054][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-06 19:01:23.056][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-06 19:01:23.058][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-06 19:01:23.060][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-06 19:01:23.062][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-06 19:01:23.064][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-06 19:01:23.066][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-06 19:01:23.068][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-06 19:01:23.070][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-06 19:01:23.072][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-06 19:01:23.074][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:01:23.075][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:01:23.076][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.079][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:23.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:23.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:23.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.105][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[2023-02-06 19:01:23.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:23.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:23.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.129][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[2023-02-06 19:01:23.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.146][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[2023-02-06 19:01:23.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.155][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[2023-02-06 19:01:23.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.163][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[2023-02-06 19:01:23.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:23.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:23.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:23.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.197][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[2023-02-06 19:01:23.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.205][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[2023-02-06 19:01:23.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:23.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.222][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[2023-02-06 19:01:23.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:23.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.230][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[2023-02-06 19:01:23.232][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-02-06 19:01:23.233][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-02-06 19:01:23.236][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:23.237][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-06 19:01:23.238][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:23.240][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:23.241][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:23.242][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-02-06 19:01:23.244][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:23.245][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:23.246][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-06 19:01:23.248][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:23.249][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:23.250][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-02-06 19:01:23.252][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-02-06 19:01:23.253][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-02-06 19:01:23.254][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:23.256][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:01:23.256][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-02-06 19:01:23.257][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-06 19:01:23.258][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:23.259][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:23.261][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:23.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:23.263][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:23.265][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:23.266][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-02-06 19:01:23.266][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-02-06 19:01:23.267][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:23.268][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:23.270][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:23.271][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:23.273][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-06 19:01:23.275][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-06 19:01:23.286][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:01:23.288][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:01:23.293][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-02-06 19:01:23.294][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-02-06 19:01:23.295][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-02-06 19:01:23.297][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-06 19:01:23.299][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:23.300][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:23.302][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-02-06 19:01:23.303][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-02-06 19:01:23.305][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-02-06 19:01:23.305][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-02-06 19:01:23.306][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:23.307][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:23.308][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-02-06 19:01:23.309][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-02-06 19:01:23.311][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-02-06 19:01:23.313][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-06 19:01:23.314][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:23.316][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:23.317][private$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[2023-02-06 19:01:23.319][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:23.320][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-02-06 19:01:23.322][biodb::testThat]
biodb.INFO [2023-02-06 19:01:23.323][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2023-02-06 19:01:23.325][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:23.326][biodb::testThat]
biodb.DEBUG[2023-02-06 19:01:23.331][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:23.333][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:23.335][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-06 19:01:23.337][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:23.338][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-06 19:01:23.343][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-06 19:01:23.345][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-06 19:01:23.346][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-06 19:01:23.348][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-06 19:01:23.351][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2023-02-06 19:01:23.354][biodb::testThat]
biodb.INFO [2023-02-06 19:01:23.355][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2023-02-06 19:01:23.356][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:23.358][biodb::testThat]
biodb.DEBUG[2023-02-06 19:01:23.360][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-02-06 19:01:23.362][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-02-06 19:01:23.364][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:23.366][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-02-06 19:01:23.368][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-02-06 19:01:23.370][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:01:23.373][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-02-06 19:01:23.375][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:23.395][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:23.397][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-06 19:01:23.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:23.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:23.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:23.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:23.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:23.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:23.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:23.417][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:23.419][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:23.420][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.421][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:23.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:23.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.441][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:23.442][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:23.443][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.445][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.446][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:23.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:23.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.456][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:23.457][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:23.458][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.460][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.462][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:23.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:23.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.471][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:23.473][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:23.474][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.475][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:23.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:23.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.486][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:23.488][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:23.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.491][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:23.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:23.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.502][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:23.503][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:23.504][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.506][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.508][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:23.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:23.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.517][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:23.518][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:23.519][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.521][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.522][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:23.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:23.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.531][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:23.533][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:23.534][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.535][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.537][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:23.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:23.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.546][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:23.548][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:23.549][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.550][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.552][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:23.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:23.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.561][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:23.563][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:23.564][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.566][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.567][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:23.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:23.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.577][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:23.578][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:23.588][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.590][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.592][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:23.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:23.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.601][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.603][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.604][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.605][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.617][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:23.618][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:23.619][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.621][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:23.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:23.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.632][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:23.633][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:23.635][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.636][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:23.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:23.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.647][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:23.648][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:23.650][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.651][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.653][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:23.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:23.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.662][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:23.664][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:23.665][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.666][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.668][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:23.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:23.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.677][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-02-06 19:01:23.679][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:23.680][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.682][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.683][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-02-06 19:01:23.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:23.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:23.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:23.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:23.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:23.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:23.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:23.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.709][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:23.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:23.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.715][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:23.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:23.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.720][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:23.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:23.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.725][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:23.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:23.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.738][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:23.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:23.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.745][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:23.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:23.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:23.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:23.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:23.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:23.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:23.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:23.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:23.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:23.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:23.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:23.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:23.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:23.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.782][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:23.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:23.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.788][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:23.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:23.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.793][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:23.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:23.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.798][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:23.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:23.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.804][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:23.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:23.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.809][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:23.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:23.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.815][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:23.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:23.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.820][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:23.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:23.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.825][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:23.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:23.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.831][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:23.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:23.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.836][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:23.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:23.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.841][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:23.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:23.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.847][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:23.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:23.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.852][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:23.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:23.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.857][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:23.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:23.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.863][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:23.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:23.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:23.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:23.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:23.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:23.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.887][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.903][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:23.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:23.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.909][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:23.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:23.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.914][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:23.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:23.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:23.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:23.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:23.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:23.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:23.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:23.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:23.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:23.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.940][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:23.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:23.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:23.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:23.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.950][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:23.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:23.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.956][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:23.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:23.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.961][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:23.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:23.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.966][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:23.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:23.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.971][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:23.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:23.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.976][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:23.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:23.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.982][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-06 19:01:23.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.987][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.992][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:23.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:23.997][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:23.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:24.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.002][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-06 19:01:24.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:24.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:24.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:24.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:24.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:24.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:24.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:24.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:24.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:24.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:24.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:24.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.051][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:24.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:24.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.056][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:24.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:24.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.067][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:24.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:24.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:24.107][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-02-06 19:01:24.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:24.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:24.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:24.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:24.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:01:24.127][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-06 19:01:24.129][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-02-06 19:01:24.130][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-02-06 19:01:24.131][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-06 19:01:24.133][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.135][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.137][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-06 19:01:24.143][biodb::testContext]
biodb.INFO [2023-02-06 19:01:24.144][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:01:24.146][biodb::testContext] Test context - Test search of entries
biodb.INFO [2023-02-06 19:01:24.147][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:01:24.148][biodb::testContext]
biodb.INFO [2023-02-06 19:01:24.164][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:01:24.166][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-06 19:01:24.171][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:01:24.172][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-06 19:01:24.174][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-06 19:01:24.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.179][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-06 19:01:24.180][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-06 19:01:24.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.185][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-06 19:01:24.186][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-06 19:01:24.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.191][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-06 19:01:24.193][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-06 19:01:24.194][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-06 19:01:24.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.199][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-06 19:01:24.200][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-06 19:01:24.202][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-06 19:01:24.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.205][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[2023-02-06 19:01:24.206][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-06 19:01:24.208][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-06 19:01:24.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.213][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-06 19:01:24.214][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-06 19:01:24.215][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-06 19:01:24.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.220][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-06 19:01:24.221][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-06 19:01:24.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.226][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-06 19:01:24.228][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-06 19:01:24.229][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-06 19:01:24.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.234][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:01:24.235][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-06 19:01:24.236][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-06 19:01:24.238][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-06 19:01:24.239][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-06 19:01:24.240][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-06 19:01:24.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.245][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-06 19:01:24.247][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-06 19:01:24.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.251][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-06 19:01:24.253][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-06 19:01:24.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.258][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-06 19:01:24.259][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-06 19:01:24.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.264][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-06 19:01:24.265][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-06 19:01:24.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.270][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-06 19:01:24.271][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-06 19:01:24.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.276][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:01:24.277][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-06 19:01:24.281][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-06 19:01:24.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.286][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-06 19:01:24.288][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-06 19:01:24.289][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-06 19:01:24.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.294][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-06 19:01:24.296][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.306][self$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[2023-02-06 19:01:24.308][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.309][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:24.311][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.312][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.313][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.314][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.316][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:01:24.317][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:24.318][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.319][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-06 19:01:24.321][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:24.322][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.323][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.325][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:01:24.325][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:01:24.325][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:01:24.325][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:01:24.325][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:01:24.326][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:24.327][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:24.328][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:24.330][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:24.331][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:24.332][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:24.333][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.335][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.336][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:24.337][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:24.338][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.340][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.341][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-06 19:01:24.343][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.345][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:01:24.346][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.347][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:24.349][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.350][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.351][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.353][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.354][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:01:24.355][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:24.357][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.358][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-06 19:01:24.359][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:24.360][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.362][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.363][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:01:24.363][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:01:24.363][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:01:24.363][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:01:24.363][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:01:24.364][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:24.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:24.367][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:24.368][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:24.369][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:24.371][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:24.372][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.373][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.375][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:24.376][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:24.377][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.378][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.380][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-06 19:01:24.382][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.384][self$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[2023-02-06 19:01:24.385][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.386][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:24.388][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.389][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.390][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.392][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.393][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:01:24.394][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:24.396][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.397][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-06 19:01:24.398][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:24.400][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.401][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.402][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.404][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:24.405][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:24.406][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:24.407][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:24.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:24.410][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:24.411][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.412][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.414][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:24.415][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:24.416][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.417][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.419][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-06 19:01:24.421][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.423][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:01:24.424][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.425][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:24.427][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.428][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.429][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.431][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.432][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:01:24.433][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:24.443][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.444][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-06 19:01:24.446][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:24.447][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.449][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.450][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.451][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:24.453][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:24.454][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:24.455][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:24.457][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:24.458][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:24.459][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.460][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.462][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:24.463][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:24.464][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.466][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.468][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:01:24.469][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.476][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[2023-02-06 19:01:24.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.482][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[2023-02-06 19:01:24.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.524][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[2023-02-06 19:01:24.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.567][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[2023-02-06 19:01:24.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.583][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-06 19:01:24.585][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-06 19:01:24.588][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-06 19:01:24.590][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-06 19:01:24.592][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:01:24.595][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-06 19:01:24.597][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-06 19:01:24.599][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-06 19:01:24.601][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-06 19:01:24.603][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-06 19:01:24.605][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:01:24.607][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-06 19:01:24.609][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-06 19:01:24.611][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-06 19:01:24.613][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-06 19:01:24.615][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:01:24.617][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-06 19:01:24.619][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-06 19:01:24.621][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:01:24.623][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-06 19:01:24.625][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-06 19:01:24.627][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-06 19:01:24.629][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-06 19:01:24.631][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-06 19:01:24.633][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-06 19:01:24.635][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-06 19:01:24.637][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-06 19:01:24.639][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-06 19:01:24.641][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-06 19:01:24.643][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-06 19:01:24.645][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-06 19:01:24.647][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-06 19:01:24.649][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-06 19:01:24.651][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-06 19:01:24.653][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-06 19:01:24.655][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-06 19:01:24.657][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-06 19:01:24.659][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-06 19:01:24.661][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-06 19:01:24.663][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-06 19:01:24.665][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-06 19:01:24.668][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-06 19:01:24.670][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-06 19:01:24.672][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-06 19:01:24.674][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-06 19:01:24.676][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-06 19:01:24.678][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-06 19:01:24.680][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-06 19:01:24.682][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-06 19:01:24.684][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-06 19:01:24.686][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-06 19:01:24.688][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-06 19:01:24.690][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-06 19:01:24.691][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-06 19:01:24.693][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-06 19:01:24.695][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-06 19:01:24.697][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-06 19:01:24.699][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-06 19:01:24.701][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-06 19:01:24.703][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-06 19:01:24.705][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-06 19:01:24.707][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-06 19:01:24.709][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-06 19:01:24.711][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-06 19:01:24.713][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-06 19:01:24.715][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-06 19:01:24.717][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:01:24.727][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:01:24.729][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-06 19:01:24.731][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-06 19:01:24.733][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-06 19:01:24.735][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-06 19:01:24.737][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-06 19:01:24.739][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-06 19:01:24.741][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-06 19:01:24.742][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-06 19:01:24.744][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-06 19:01:24.746][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-06 19:01:24.748][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-06 19:01:24.750][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-06 19:01:24.752][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-06 19:01:24.754][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-06 19:01:24.756][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-06 19:01:24.758][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-06 19:01:24.760][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:01:24.761][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:01:24.762][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.765][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.833][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[2023-02-06 19:01:24.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.850][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[2023-02-06 19:01:24.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:24.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:24.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:24.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:24.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:24.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:24.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:24.920][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-02-06 19:01:24.922][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-02-06 19:01:24.924][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.925][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.927][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.928][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:24.929][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.931][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-02-06 19:01:24.932][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.933][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.935][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-02-06 19:01:24.936][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:24.938][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.939][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-02-06 19:01:24.940][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-02-06 19:01:24.942][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-02-06 19:01:24.943][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:24.944][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:01:24.944][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-02-06 19:01:24.946][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-02-06 19:01:24.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:24.948][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:24.950][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:24.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:24.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:24.953][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:24.955][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-02-06 19:01:24.955][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-02-06 19:01:24.956][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:24.957][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:24.958][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:24.960][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:24.962][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-06 19:01:24.964][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-06 19:01:24.966][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:01:24.968][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:01:24.972][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-02-06 19:01:24.974][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-02-06 19:01:24.975][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-02-06 19:01:24.977][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-06 19:01:24.979][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:24.980][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:24.982][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-02-06 19:01:24.983][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-02-06 19:01:24.984][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-02-06 19:01:24.984][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-02-06 19:01:24.986][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:24.987][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:24.988][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-02-06 19:01:24.989][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-02-06 19:01:24.991][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-02-06 19:01:25.007][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-06 19:01:25.008][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:25.010][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:25.012][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.17-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-02-06 19:01:25.014][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-02-06 19:01:25.015][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-02-06 19:01:25.017][biodb::testThat]
biodb.INFO [2023-02-06 19:01:25.018][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2023-02-06 19:01:25.020][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:25.021][biodb::testThat]
biodb.DEBUG[2023-02-06 19:01:25.034][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-02-06 19:01:25.036][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2023-02-06 19:01:25.037][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2023-02-06 19:01:25.041][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:25.043][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:25.045][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-06 19:01:25.047][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:25.048][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-06 19:01:25.053][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-06 19:01:25.055][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-06 19:01:25.056][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-06 19:01:25.057][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-06 19:01:25.059][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-02-06 19:01:25.060][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2023-02-06 19:01:25.062][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-02-06 19:01:25.064][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-02-06 19:01:25.066][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:25.068][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-02-06 19:01:25.071][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-02-06 19:01:25.072][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:01:25.075][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-02-06 19:01:25.076][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:25.096][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:25.098][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-06 19:01:25.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:25.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:25.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:25.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:25.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:25.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:25.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:25.119][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.120][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.122][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.123][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.134][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.135][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.136][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.138][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.140][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.149][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.159][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.160][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.162][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.164][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.173][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.175][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.176][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.177][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.189][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.190][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.192][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.193][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.204][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:25.206][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:25.207][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.208][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.210][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:25.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:25.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.219][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:25.221][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:25.222][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.223][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.225][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:25.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:25.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.235][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:25.236][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:25.237][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.239][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.241][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:25.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:25.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.250][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:25.251][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:25.253][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.254][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.256][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:25.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:25.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.265][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:25.267][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:25.268][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.269][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.271][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:25.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:25.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.280][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:25.282][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:25.283][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.284][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.286][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:25.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:25.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.296][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.297][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.298][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.300][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.319][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:25.321][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:25.323][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.324][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:25.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:25.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.335][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:25.337][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:25.338][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.340][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:25.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:25.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.351][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:25.352][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:25.353][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.355][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.357][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:25.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:25.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.366][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:25.367][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:25.369][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.370][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.372][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:25.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:25.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.381][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-02-06 19:01:25.383][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:25.384][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.385][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.387][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-02-06 19:01:25.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:25.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.414][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.419][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.425][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.430][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.436][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.441][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.488][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:25.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:25.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.493][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:25.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:25.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:25.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:25.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.504][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:25.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:25.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.509][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:25.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:25.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.514][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:25.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:25.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.520][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:25.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:25.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.525][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:25.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:25.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.530][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:25.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:25.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.535][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:25.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:25.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.541][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:25.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:25.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.546][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:25.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:25.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.551][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:25.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:25.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.557][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:25.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:25.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.562][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:25.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:25.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:25.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:25.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:25.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:25.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.578][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:25.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:25.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.600][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:25.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:25.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.614][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:25.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:25.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.620][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:25.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:25.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:25.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:25.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:25.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:25.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:25.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:25.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:25.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:25.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:25.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:25.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:25.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:25.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.658][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:25.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:25.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.663][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:25.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:25.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.669][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:25.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:25.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.674][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:25.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:25.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.680][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:25.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:25.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.685][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:25.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:25.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.691][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-06 19:01:25.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.707][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.712][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-06 19:01:25.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:25.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:25.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:25.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.728][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:25.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:25.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:25.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:25.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.739][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:25.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:25.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.744][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:25.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:25.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.763][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:25.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:25.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.769][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:25.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:25.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.780][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:25.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:25.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:25.822][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-02-06 19:01:25.824][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:25.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:25.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.830][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:25.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:25.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.835][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:25.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:25.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.841][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:25.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:25.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:25.847][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-06 19:01:25.848][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-02-06 19:01:25.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:25.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:25.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:25.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:25.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:25.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:25.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:25.865][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-02-06 19:01:25.866][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-02-06 19:01:25.869][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:25.870][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-02-06 19:01:25.873][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-02-06 19:01:25.875][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:01:25.877][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-02-06 19:01:25.878][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:25.907][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:25.909][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-02-06 19:01:25.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:25.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:25.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:25.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:25.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:25.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:25.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:25.929][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.931][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.932][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.933][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:25.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:25.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.944][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.946][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.947][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.948][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.950][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:25.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.959][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.961][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.962][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.964][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.965][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:25.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.974][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.976][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.977][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.979][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:25.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.990][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.991][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.993][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:25.994][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:25.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:25.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.005][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:26.006][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:26.008][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.009][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.011][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:26.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:26.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.020][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:26.022][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:26.023][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.024][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.026][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:26.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:26.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.035][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:26.037][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:26.038][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.039][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.041][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:26.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:26.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.059][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:26.060][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:26.062][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.063][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.065][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:26.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:26.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.075][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:26.076][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:26.078][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.079][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.081][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:26.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:26.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.090][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:26.092][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:26.093][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.094][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.096][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:26.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:26.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.105][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.107][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.108][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.109][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.121][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.122][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.123][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.125][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.136][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:26.137][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:26.139][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.140][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.142][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:26.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:26.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.151][ef$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.152][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.154][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.155][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.157][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.166][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:26.167][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:26.169][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.170][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.172][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:26.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:26.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.181][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-02-06 19:01:26.183][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:26.184][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.185][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.187][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-02-06 19:01:26.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:26.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.222][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:26.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:26.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.228][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:26.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:26.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.233][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:01:26.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:01:26.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.238][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:26.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:26.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.244][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:26.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:26.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.249][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-02-06 19:01:26.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-02-06 19:01:26.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:26.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:26.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:26.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:26.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:26.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:26.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:26.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:26.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:26.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:26.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:26.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-02-06 19:01:26.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.288][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:26.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:26.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.293][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:26.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:26.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.298][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:26.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:26.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.304][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:26.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:26.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.309][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:26.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:26.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.315][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:26.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-02-06 19:01:26.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.320][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:26.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:26.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.326][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:26.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:26.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.331][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:26.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-02-06 19:01:26.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.337][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.342][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.348][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.362][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:26.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:26.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.368][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:26.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:26.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.373][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:26.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:26.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.378][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:26.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:26.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:26.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:26.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.389][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-02-06 19:01:26.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-02-06 19:01:26.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.399][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.410][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:26.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:26.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.415][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:26.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:26.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.421][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:26.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:26.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:26.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:26.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:26.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.447][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:26.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:26.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:26.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:26.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.458][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:26.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:26.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.463][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:26.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:26.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.469][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:26.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:26.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.475][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:26.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:26.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.480][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:26.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:26.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.485][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-02-06 19:01:26.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-02-06 19:01:26.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.499][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-06 19:01:26.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.516][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.521][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-02-06 19:01:26.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-02-06 19:01:26.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.531][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:26.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:26.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.537][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:26.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:26.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:26.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:26.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.548][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:26.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:26.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:26.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:26.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.562][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:26.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:26.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.568][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:26.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:26.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.579][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:26.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:26.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:26.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:26.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:26.621][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-02-06 19:01:26.622][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.628][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.633][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.648][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:26.653][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-06 19:01:26.655][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2023-02-06 19:01:26.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:26.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:26.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:26.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:26.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:26.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:26.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:26.686][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-02-06 19:01:26.687][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-02-06 19:01:26.689][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-02-06 19:01:26.691][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:26.693][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:26.695][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-06 19:01:26.697][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:26.698][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-06 19:01:26.703][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-06 19:01:26.705][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-06 19:01:26.706][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-06 19:01:26.708][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-06 19:01:26.709][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-02-06 19:01:26.710][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-02-06 19:01:26.713][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.718][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.724][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.729][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.735][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.740][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.746][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:26.751][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-06 19:01:26.752][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-02-06 19:01:26.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:26.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:26.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:26.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:26.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:26.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:26.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:26.769][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.774][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.780][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.794][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.800][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.805][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.811][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:26.816][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-02-06 19:01:26.817][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-02-06 19:01:26.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:26.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:26.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:26.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:26.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:26.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:26.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:26.848][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-02-06 19:01:26.849][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-02-06 19:01:26.850][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-02-06 19:01:26.853][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:26.855][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:26.857][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-02-06 19:01:26.858][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-02-06 19:01:26.860][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-02-06 19:01:26.865][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-02-06 19:01:26.867][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-02-06 19:01:26.868][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-02-06 19:01:26.869][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-02-06 19:01:26.871][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-02-06 19:01:26.872][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-02-06 19:01:26.874][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.880][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.885][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.891][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.896][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.901][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.907][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:26.912][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-02-06 19:01:26.913][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2023-02-06 19:01:26.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:26.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:26.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:26.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:26.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:26.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:26.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:26.930][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.944][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.950][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.956][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.961][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.966][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:26.972][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-02-06 19:01:26.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-02-06 19:01:26.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:26.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:26.977][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-02-06 19:01:26.978][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-02-06 19:01:26.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:26.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:26.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:26.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:26.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:26.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:26.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-06 19:01:26.998][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-06 19:01:27.000][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-02-06 19:01:27.001][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-02-06 19:01:27.003][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-06 19:01:27.004][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:27.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:27.006][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:27.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:27.009][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:27.010][FUN] Functions in observer 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
12.764 0.306 17.740
biodbHmdb.Rcheck/biodbHmdb-Ex.timings
| name | user | system | elapsed | |
| HmdbMetabolitesConn | 2.049 | 0.195 | 2.243 | |
| HmdbMetabolitesEntry | 0.418 | 0.004 | 0.474 | |