| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:22 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the biodbHmdb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbHmdb.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 196/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbHmdb 1.5.1 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: biodbHmdb |
| Version: 1.5.1 |
| 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/site-library --timings biodbHmdb_1.5.1.tar.gz |
| StartedAt: 2023-04-11 18:52:30 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 18:53:30 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 60.0 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/site-library --timings biodbHmdb_1.5.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbHmdb.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.5.1’
* 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 ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘biodbHmdb.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
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/site-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++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c Tag.cpp -o Tag.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractXmlEntries.cpp -o extractXmlEntries.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-100-tag.cpp -o test-100-tag.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -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/site-library/00LOCK-biodbHmdb/00new/biodbHmdb/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbHmdb)
biodbHmdb.Rcheck/tests/testthat.Rout
R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2023-04-11 18:53:11.903][biodb::testContext]
biodb.INFO [2023-04-11 18:53:11.906][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:53:11.907][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2023-04-11 18:53:11.908][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:53:11.909][biodb::testContext]
biodb.INFO [2023-04-11 18:53:11.911][biodb::testThat]
biodb.INFO [2023-04-11 18:53:11.912][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2023-04-11 18:53:11.913][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:11.914][biodb::testThat]
biodb.INFO [2023-04-11 18:53:12.016][biodb::testContext]
biodb.INFO [2023-04-11 18:53:12.017][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:53:12.018][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-04-11 18:53:12.019][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:53:12.020][biodb::testContext]
biodb.INFO [2023-04-11 18:53:12.038][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:53:12.040][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-11 18:53:12.048][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:12.049][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-11 18:53:12.050][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-11 18:53:12.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.055][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-11 18:53:12.073][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-11 18:53:12.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.078][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-11 18:53:12.079][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-11 18:53:12.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.082][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-11 18:53:12.084][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-11 18:53:12.085][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-11 18:53:12.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.088][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-11 18:53:12.090][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-11 18:53:12.091][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-11 18:53:12.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.095][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-11 18:53:12.096][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-11 18:53:12.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.100][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-11 18:53:12.101][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-11 18:53:12.102][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-11 18:53:12.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.106][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-11 18:53:12.107][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-11 18:53:12.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.111][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-11 18:53:12.112][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-11 18:53:12.113][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-11 18:53:12.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.117][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:53:12.128][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-11 18:53:12.129][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-11 18:53:12.130][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-11 18:53:12.131][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-11 18:53:12.132][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-11 18:53:12.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.136][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-11 18:53:12.137][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-11 18:53:12.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.140][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-11 18:53:12.141][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-11 18:53:12.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.145][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-11 18:53:12.146][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-11 18:53:12.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.149][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-11 18:53:12.150][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-11 18:53:12.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.154][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-11 18:53:12.155][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-11 18:53:12.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.158][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:53:12.159][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-11 18:53:12.162][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-11 18:53:12.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.166][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-11 18:53:12.167][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-11 18:53:12.168][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-11 18:53:12.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.174][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-11 18:53:12.206][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.221][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-11 18:53:12.222][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.223][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:12.224][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.225][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.226][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.227][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.228][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:53:12.229][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:12.230][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.231][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-11 18:53:12.232][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:12.233][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.234][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.235][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:12.235][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:53:12.235][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:53:12.235][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:53:12.235][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:53:12.236][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:12.237][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:12.238][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:12.238][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:12.239][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:12.240][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:12.241][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.242][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.243][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:12.244][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:12.245][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.246][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.247][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-11 18:53:12.249][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.250][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:53:12.250][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.251][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:12.252][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.253][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.254][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.255][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.256][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:53:12.257][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:12.258][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.259][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-11 18:53:12.260][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:12.261][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.262][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.263][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:12.263][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:53:12.263][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:53:12.263][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:53:12.263][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:53:12.264][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:12.265][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:12.266][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:12.267][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:12.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:12.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:12.269][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.270][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.271][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:12.272][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:12.273][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.274][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.275][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-11 18:53:12.277][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.278][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-11 18:53:12.279][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.280][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:12.281][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.282][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.283][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.283][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.284][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:53:12.285][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:12.286][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.287][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-11 18:53:12.288][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:12.295][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.296][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.297][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.298][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:12.299][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:12.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:12.300][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:12.301][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:12.302][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:12.303][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.304][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.305][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:12.306][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:12.307][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.308][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.309][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-11 18:53:12.311][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.311][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:53:12.312][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.313][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:12.314][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.315][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.316][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.317][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.318][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:53:12.319][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:12.320][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.321][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-11 18:53:12.322][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:12.323][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.324][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.325][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.326][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:12.327][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:12.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:12.328][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:12.329][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:12.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:12.331][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.332][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.333][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:12.334][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:12.335][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.336][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.340][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:12.341][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.415][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-11 18:53:12.420][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-11 18:53:12.421][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-11 18:53:12.423][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-11 18:53:12.424][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:53:12.425][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-11 18:53:12.427][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-11 18:53:12.428][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-11 18:53:12.429][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-11 18:53:12.430][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-11 18:53:12.432][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:53:12.433][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-11 18:53:12.434][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-11 18:53:12.436][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-11 18:53:12.437][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-11 18:53:12.438][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:53:12.440][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-11 18:53:12.441][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-11 18:53:12.442][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:53:12.444][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-11 18:53:12.445][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-11 18:53:12.446][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-11 18:53:12.448][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-11 18:53:12.449][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-11 18:53:12.450][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-11 18:53:12.451][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-11 18:53:12.453][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-11 18:53:12.454][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-11 18:53:12.455][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-11 18:53:12.463][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-11 18:53:12.464][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-11 18:53:12.466][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-11 18:53:12.467][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-11 18:53:12.468][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-11 18:53:12.470][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-11 18:53:12.471][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-11 18:53:12.472][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-11 18:53:12.473][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-11 18:53:12.475][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-11 18:53:12.476][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-11 18:53:12.477][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-11 18:53:12.479][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-11 18:53:12.480][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-11 18:53:12.481][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-11 18:53:12.483][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-11 18:53:12.484][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-11 18:53:12.485][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-11 18:53:12.487][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-11 18:53:12.488][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-11 18:53:12.489][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-11 18:53:12.491][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-11 18:53:12.492][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-11 18:53:12.493][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-11 18:53:12.495][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-11 18:53:12.496][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-11 18:53:12.497][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-11 18:53:12.499][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-11 18:53:12.500][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-11 18:53:12.501][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-11 18:53:12.503][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-11 18:53:12.504][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-11 18:53:12.505][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-11 18:53:12.506][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-11 18:53:12.508][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-11 18:53:12.509][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-11 18:53:12.510][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-11 18:53:12.512][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:53:12.513][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:53:12.514][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-11 18:53:12.516][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-11 18:53:12.517][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-11 18:53:12.518][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-11 18:53:12.520][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-11 18:53:12.521][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-11 18:53:12.522][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-11 18:53:12.524][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-11 18:53:12.525][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-11 18:53:12.526][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-11 18:53:12.528][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-11 18:53:12.529][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-11 18:53:12.530][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-11 18:53:12.532][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-11 18:53:12.533][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-11 18:53:12.539][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-11 18:53:12.540][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:53:12.544][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:12.545][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.546][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.569][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[2023-04-11 18:53:12.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.593][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[2023-04-11 18:53:12.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.599][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[2023-04-11 18:53:12.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.666][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[2023-04-11 18:53:12.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.672][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[2023-04-11 18:53:12.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:12.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:12.692][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-04-11 18:53:12.702][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-04-11 18:53:12.704][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.705][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.706][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.707][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:12.708][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.709][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-04-11 18:53:12.710][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.711][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.712][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-11 18:53:12.713][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:12.714][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.714][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-04-11 18:53:12.715][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-04-11 18:53:12.716][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-04-11 18:53:12.718][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:12.719][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:12.719][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-04-11 18:53:12.719][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2023-04-11 18:53:12.720][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-11 18:53:12.721][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:12.722][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:12.723][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:12.724][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:12.724][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:12.725][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:12.726][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-11 18:53:12.726][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-04-11 18:53:12.727][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:12.728][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:12.729][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:12.730][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:12.736][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2023-04-11 18:53:12.737][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-11 18:53:12.739][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-11 18:53:12.740][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:53:12.742][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:53:12.765][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-04-11 18:53:12.766][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-04-11 18:53:12.771][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-11 18:53:12.775][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-11 18:53:12.779][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:12.780][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:12.782][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-04-11 18:53:12.783][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-04-11 18:53:12.784][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-11 18:53:12.784][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-04-11 18:53:12.785][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:12.786][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:12.786][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-04-11 18:53:12.787][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-04-11 18:53:12.788][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-11 18:53:12.804][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-11 18:53:12.806][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:12.807][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:12.808][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-11 18:53:12.809][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:12.810][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-04-11 18:53:12.833][biodb::testThat]
biodb.INFO [2023-04-11 18:53:12.834][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-04-11 18:53:12.835][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:12.836][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:12.840][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2023-04-11 18:53:12.845][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:12.848][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-11 18:53:12.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:12.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:12.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:12.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:12.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:12.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:12.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:12.879][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.880][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.881][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.882][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:12.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:12.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.902][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:12.903][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:12.904][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.905][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.930][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:12.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:12.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.937][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:12.938][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:12.939][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.939][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.941][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:12.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:12.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.947][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:12.948][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:12.949][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.950][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.952][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:12.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:12.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.958][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.959][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.960][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.961][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:12.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.969][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:12.970][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:12.971][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.972][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:12.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:12.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.980][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:12.981][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:12.982][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.991][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.992][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:12.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:12.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:12.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:12.999][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.000][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.001][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.002][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.004][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.010][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.012][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.012][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.013][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.015][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.022][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.023][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.024][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.025][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.026][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.033][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:13.034][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:13.035][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.036][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.037][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:13.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:13.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.044][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.045][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.046][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.047][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.056][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.057][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.058][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.059][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.068][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.069][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.070][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.071][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.079][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.080][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.081][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.082][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.090][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:13.091][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:13.092][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.093][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.094][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:13.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:13.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.101][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.102][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.103][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.104][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.105][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.112][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-11 18:53:13.113][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.114][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.114][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.116][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-11 18:53:13.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.172][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.176][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.180][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.184][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:13.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:13.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.188][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:13.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:13.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.191][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:13.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:13.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.218][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.222][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.226][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.230][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.233][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.237][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.241][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.245][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.249][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.252][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:13.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:13.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.256][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:13.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:13.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.260][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:13.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:13.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.264][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:13.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:13.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.272][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:13.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:13.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.275][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:13.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:13.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.287][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.291][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.298][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.302][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.306][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.310][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.333][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.337][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.341][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.345][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.349][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.353][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.357][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.361][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.364][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.368][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.372][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-11 18:53:13.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.376][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.387][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-11 18:53:13.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:13.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.430][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.437][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.441][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.448][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:13.479][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2023-04-11 18:53:13.484][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:13.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:13.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.488][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:13.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:13.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.492][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:13.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:13.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.496][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:13.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:13.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.523][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.561][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.565][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.569][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:13.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.593][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.595][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.595][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.596][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:13.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:13.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.608][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.612][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.616][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.620][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.621][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.622][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.623][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.624][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:13.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.646][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.647][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.648][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.649][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:13.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.661][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.665][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.669][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.673][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.674][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.675][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.676][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.677][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:13.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.706][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.707][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.708][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.709][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:13.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.721][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.725][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.729][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.733][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.734][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.735][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.736][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.737][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:13.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.748][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.755][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.759][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.760][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.761][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.762][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:13.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:13.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.774][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:13.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:13.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.778][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:13.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:13.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.782][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:13.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:13.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.786][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:13.787][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:13.788][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.789][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.790][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:13.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:13.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.800][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:13.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:13.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.804][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:13.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:13.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.808][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:13.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:13.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.812][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:13.813][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:13.814][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.815][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.816][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:13.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:13.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.831][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.835][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.839][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.843][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.844][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.845][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.846][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.847][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:13.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.869][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.870][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.871][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.872][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:13.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.884][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.888][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.892][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.896][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.897][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.898][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.899][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:13.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.911][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.915][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.919][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.923][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.924][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.925][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.925][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.926][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:13.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.937][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.941][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.945][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.949][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.950][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.952][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.953][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:13.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.968][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.972][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.975][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.979][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.980][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.981][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.982][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.983][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:13.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:13.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.994][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:13.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:13.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:13.998][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:13.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:14.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.002][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:14.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:14.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.006][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:14.007][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:14.008][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.009][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.010][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:14.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:14.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.020][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.032][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.033][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.034][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.035][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.047][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.052][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.056][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.059][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.060][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.061][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.062][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.063][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.074][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:14.075][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:14.076][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.077][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.082][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:14.083][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:14.084][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.085][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.094][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.096][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.097][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.097][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.102][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:14.103][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:14.104][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.105][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.111][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:14.112][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:14.113][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.114][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.119][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:14.120][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:14.121][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.122][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.127][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:14.128][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:14.129][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.130][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.135][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:14.136][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:14.137][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.138][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.143][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:14.144][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:14.145][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.146][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.151][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:14.152][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:14.153][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.154][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.159][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:14.160][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:14.161][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.162][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.167][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.168][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.169][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.170][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.175][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:14.176][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:14.177][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.178][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.183][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:14.184][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:14.185][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.186][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.191][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.192][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.193][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.194][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.199][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:14.201][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:14.201][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.202][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.207][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:14.209][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:14.210][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.210][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.215][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:14.217][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:14.217][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.218][ef$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:14.229][biodb::testThat]
biodb.INFO [2023-04-11 18:53:14.230][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-11 18:53:14.231][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:14.232][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:14.245][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-04-11 18:53:14.253][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-11 18:53:14.258][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:14.260][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-11 18:53:14.262][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-04-11 18:53:14.264][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:14.266][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-04-11 18:53:14.267][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:14.310][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:14.312][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-11 18:53:14.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:14.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:14.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:14.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:14.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:14.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:14.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:14.327][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:14.328][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:14.329][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.330][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:14.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:14.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.338][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:14.339][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:14.340][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.341][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.342][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:14.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:14.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.349][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:14.350][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:14.351][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.352][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.353][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:14.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:14.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.369][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.370][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.371][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.372][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.373][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.380][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:14.381][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:14.382][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.383][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:14.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:14.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.391][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:14.393][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:14.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.395][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:14.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:14.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.404][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:14.405][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:14.406][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.407][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.408][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:14.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:14.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.415][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:14.416][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:14.417][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.418][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.419][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:14.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:14.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.427][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:14.428][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:14.429][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.430][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.432][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:14.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:14.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.439][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:14.440][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:14.441][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.442][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.443][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:14.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:14.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.450][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:14.452][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:14.453][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.453][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.455][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:14.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:14.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.461][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:14.463][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:14.463][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.464][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:14.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:14.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.472][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.473][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.474][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.475][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.483][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:14.484][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:14.485][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.486][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:14.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:14.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.494][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.495][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.496][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.497][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.505][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:14.511][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:14.512][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.513][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.514][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:14.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:14.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.521][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:14.522][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:14.523][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.524][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.526][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:14.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:14.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.533][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-11 18:53:14.535][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:14.536][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.537][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.538][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-11 18:53:14.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:14.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:14.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:14.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:14.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:14.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:14.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:14.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.558][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:14.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:14.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.562][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:14.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:14.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.566][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:14.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:14.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.570][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.574][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.577][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:14.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:14.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:14.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:14.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:14.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:14.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:14.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:14.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:14.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:14.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:14.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:14.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:14.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.606][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:14.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:14.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.610][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:14.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:14.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.614][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:14.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:14.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.617][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:14.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:14.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.621][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:14.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:14.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.625][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:14.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:14.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.629][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:14.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:14.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.633][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:14.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:14.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.636][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:14.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:14.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.640][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:14.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:14.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.650][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:14.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:14.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.654][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:14.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:14.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.659][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:14.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:14.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.663][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:14.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:14.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.667][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:14.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:14.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:14.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:14.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:14.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:14.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:14.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:14.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.695][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:14.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:14.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.699][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:14.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:14.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.703][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:14.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:14.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:14.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:14.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:14.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:14.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:14.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:14.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.718][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.726][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.730][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:14.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:14.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.734][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:14.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:14.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.740][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:14.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:14.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.745][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:14.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:14.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.749][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:14.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:14.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.753][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:14.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:14.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.757][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:14.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:14.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.761][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:14.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:14.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.765][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:14.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:14.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.769][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-11 18:53:14.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.789][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-11 18:53:14.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:14.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.805][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.821][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:14.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:14.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.825][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:14.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:14.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:14.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:14.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.833][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:14.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:14.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:14.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:14.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:14.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:14.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:14.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:14.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:14.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:14.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:14.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:14.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:14.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:14.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:14.864][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-04-11 18:53:14.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-11 18:53:14.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-11 18:53:14.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-11 18:53:14.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-11 18:53:14.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-11 18:53:14.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-11 18:53:14.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:14.882][biodb::testThat]
biodb.INFO [2023-04-11 18:53:14.883][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-11 18:53:14.884][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:14.885][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:14.887][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.888][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.889][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.890][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:14.891][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2023-04-11 18:53:14.923][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.931][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:14.937][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2023-04-11 18:53:14.946][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-04-11 18:53:14.947][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-04-11 18:53:14.948][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-04-11 18:53:14.949][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:14.951][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:14.952][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-11 18:53:14.954][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:14.955][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-11 18:53:14.959][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-11 18:53:14.960][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-11 18:53:14.961][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-11 18:53:14.962][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-11 18:53:14.963][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-11 18:53:14.964][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-11 18:53:14.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:14.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:14.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:14.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:14.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:14.981][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-11 18:53:14.982][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-11 18:53:14.983][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2023-04-11 18:53:14.996][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:14.998][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:14.999][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.000][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:15.001][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2023-04-11 18:53:15.014][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:15.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:15.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.018][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:15.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:15.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.022][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:15.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:15.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:15.028][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.".
biodb.DEBUG[2023-04-11 18:53:15.095][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-04-11 18:53:15.097][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2023-04-11 18:53:15.098][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2023-04-11 18:53:15.113][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:15.115][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:15.116][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-11 18:53:15.118][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:15.119][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-11 18:53:15.138][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-11 18:53:15.139][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-11 18:53:15.140][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-11 18:53:15.141][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-11 18:53:15.142][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-11 18:53:15.143][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-11 18:53:15.145][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:15.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:15.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.149][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:15.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:15.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.153][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:15.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:15.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.163][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:15.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:15.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:15.167][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-11 18:53:15.168][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-11 18:53:15.169][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2023-04-11 18:53:15.182][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.184][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.185][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.186][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:15.187][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2023-04-11 18:53:15.202][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.206][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.210][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:15.216][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2023-04-11 18:53:15.226][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2023-04-11 18:53:15.227][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2023-04-11 18:53:15.228][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2023-04-11 18:53:15.230][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:15.231][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:15.233][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-11 18:53:15.234][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:15.235][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-11 18:53:15.240][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-11 18:53:15.241][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-11 18:53:15.242][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-11 18:53:15.243][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-11 18:53:15.244][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-11 18:53:15.245][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-11 18:53:15.247][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.251][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.255][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.259][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:15.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:15.263][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-11 18:53:15.264][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-11 18:53:15.265][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2023-04-11 18:53:15.281][biodb::testThat]
biodb.INFO [2023-04-11 18:53:15.282][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-04-11 18:53:15.283][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:15.284][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:15.309][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:15.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:15.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:15.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:15.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.317][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:15.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:15.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:15.338][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-04-11 18:53:15.339][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-04-11 18:53:15.341][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-04-11 18:53:15.342][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:15.344][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:15.345][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-11 18:53:15.347][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:15.348][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-11 18:53:15.352][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-11 18:53:15.353][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-11 18:53:15.354][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-11 18:53:15.355][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-11 18:53:15.356][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-11 18:53:15.357][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-11 18:53:15.359][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:15.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:15.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.363][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:15.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:15.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:15.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:15.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.371][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:15.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:15.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:15.375][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-11 18:53:15.376][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2023-04-11 18:53:15.392][biodb::testThat]
biodb.INFO [2023-04-11 18:53:15.393][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-04-11 18:53:15.394][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:15.395][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:15.423][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:15.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:15.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.427][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:15.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:15.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.431][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:15.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:15.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.441][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:15.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:15.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.491][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:15.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:15.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.496][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:15.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:15.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.500][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:15.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:15.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:15.504][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:15.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:15.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:15.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:15.511][biodb::testThat]
biodb.INFO [2023-04-11 18:53:15.512][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-11 18:53:15.513][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:15.514][biodb::testThat]
biodb.INFO [2023-04-11 18:53:15.520][biodb::testThat]
biodb.INFO [2023-04-11 18:53:15.521][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-11 18:53:15.521][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:15.522][biodb::testThat]
biodb.INFO [2023-04-11 18:53:15.527][biodb::testThat]
biodb.INFO [2023-04-11 18:53:15.528][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-11 18:53:15.529][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:15.530][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:15.533][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2023-04-11 18:53:16.808][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2023-04-11 18:53:16.863][biodb::testThat]
biodb.INFO [2023-04-11 18:53:16.865][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-11 18:53:16.867][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:16.869][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:17.136][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2023-04-11 18:53:17.197][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:17.200][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:17.203][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.205][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.206][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:17.208][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:17.209][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.211][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.212][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:17.214][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:17.215][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.217][ef$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:17.219][biodb::testThat]
biodb.INFO [2023-04-11 18:53:17.221][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-04-11 18:53:17.222][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:17.223][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:17.227][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-04-11 18:53:17.296][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-11 18:53:17.299][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:17.301][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-11 18:53:17.361][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-04-11 18:53:17.363][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:17.364][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:17.365][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:17.367][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:17.386][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:17.388][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-11 18:53:17.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:17.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:17.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:17.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.400][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:17.403][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:17.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:17.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.407][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:17.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:17.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:17.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:17.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:17.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:17.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:17.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:17.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:17.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:17.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:17.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:17.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:17.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:17.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:17.434][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-04-11 18:53:17.435][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-04-11 18:53:17.450][biodb::testThat]
biodb.INFO [2023-04-11 18:53:17.452][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-04-11 18:53:17.453][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:17.454][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:17.467][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2023-04-11 18:53:17.469][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2023-04-11 18:53:17.470][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-11 18:53:17.471][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:17.473][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-11 18:53:17.475][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2023-04-11 18:53:17.476][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:53:17.477][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:53:17.478][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:17.480][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:17.499][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:17.500][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-11 18:53:17.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:17.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:17.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:17.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:17.515][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:17.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:17.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.519][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:17.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:17.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:17.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:17.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:17.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:17.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:17.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:17.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:17.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:17.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:17.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:17.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:17.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:17.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:17.546][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-04-11 18:53:17.547][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-04-11 18:53:17.548][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2023-04-11 18:53:17.560][biodb::testThat]
biodb.INFO [2023-04-11 18:53:17.561][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-04-11 18:53:17.562][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:17.563][biodb::testThat]
biodb.INFO [2023-04-11 18:53:17.588][biodb::testThat]
biodb.INFO [2023-04-11 18:53:17.590][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-04-11 18:53:17.591][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:17.591][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:17.594][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:17.596][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:17.597][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-11 18:53:17.598][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:17.599][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-11 18:53:17.604][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-11 18:53:17.605][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-11 18:53:17.606][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-11 18:53:17.607][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2023-04-11 18:53:17.613][biodb::testThat]
biodb.INFO [2023-04-11 18:53:17.614][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-04-11 18:53:17.615][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:17.616][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:17.618][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:17.620][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:17.621][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-11 18:53:17.623][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:17.624][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-11 18:53:17.628][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-11 18:53:17.629][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-11 18:53:17.630][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-11 18:53:17.631][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2023-04-11 18:53:17.644][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:17.645][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:17.646][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.647][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.648][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:17.649][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:17.650][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.651][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:17.652][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:17.653][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:17.654][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:17.655][ef$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:17.656][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-11 18:53:17.657][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-04-11 18:53:17.665][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-04-11 18:53:17.666][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-11 18:53:17.667][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:17.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:17.669][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.671][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.672][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.INFO [2023-04-11 18:53:17.676][biodb::testContext]
biodb.INFO [2023-04-11 18:53:17.677][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:53:17.678][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2023-04-11 18:53:17.679][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:53:17.686][biodb::testContext]
biodb.INFO [2023-04-11 18:53:17.693][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:53:17.695][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-11 18:53:17.699][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:17.700][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-11 18:53:17.701][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-11 18:53:17.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.705][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-11 18:53:17.706][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-11 18:53:17.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.710][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-11 18:53:17.711][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-11 18:53:17.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.714][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-11 18:53:17.715][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-11 18:53:17.716][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-11 18:53:17.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.720][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-11 18:53:17.721][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-11 18:53:17.722][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-11 18:53:17.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.726][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-11 18:53:17.727][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-11 18:53:17.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.731][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-11 18:53:17.732][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-11 18:53:17.733][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-11 18:53:17.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.736][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-11 18:53:17.737][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-11 18:53:17.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.741][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-11 18:53:17.742][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-11 18:53:17.743][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-11 18:53:17.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.747][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:53:17.748][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-11 18:53:17.749][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-11 18:53:17.749][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-11 18:53:17.750][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-11 18:53:17.752][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-11 18:53:17.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.755][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-11 18:53:17.756][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-11 18:53:17.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.760][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-11 18:53:17.761][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-11 18:53:17.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.764][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-11 18:53:17.765][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-11 18:53:17.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.769][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-11 18:53:17.770][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-11 18:53:17.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.774][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-11 18:53:17.775][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-11 18:53:17.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.778][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:53:17.779][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-11 18:53:17.783][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-11 18:53:17.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.787][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-11 18:53:17.788][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-11 18:53:17.789][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-11 18:53:17.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.799][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-11 18:53:17.801][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:17.802][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-11 18:53:17.803][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.804][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:17.805][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.806][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:17.807][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:17.808][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:17.809][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:53:17.810][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:17.811][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.812][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-11 18:53:17.813][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:17.814][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.815][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.816][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:17.816][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:53:17.816][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:53:17.816][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:53:17.816][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:53:17.817][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:17.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:17.819][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:17.820][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:17.821][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:17.822][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:17.823][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:17.824][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.825][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:17.825][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:17.826][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:17.827][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.829][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-11 18:53:17.830][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:17.831][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:53:17.832][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.833][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:17.834][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.835][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:17.836][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:17.837][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:17.838][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:53:17.839][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:17.840][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.841][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-11 18:53:17.842][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:17.843][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.844][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.845][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:17.845][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:53:17.845][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:53:17.845][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:53:17.845][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:53:17.846][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:17.847][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:17.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:17.849][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:17.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:17.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:17.852][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:17.853][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.853][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:17.854][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:17.855][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:17.856][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.857][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-11 18:53:17.859][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.860][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-11 18:53:17.861][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.862][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:17.863][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.864][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:17.865][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:17.866][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:17.867][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:53:17.868][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:17.869][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:17.870][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-11 18:53:17.871][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:17.872][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.873][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.874][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.875][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:17.876][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:17.877][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:17.877][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:17.878][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:17.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:17.880][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:17.881][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.882][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:17.883][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:17.884][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:17.885][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.886][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-11 18:53:17.888][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.889][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:53:17.890][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.891][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:17.892][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.893][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:17.894][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:17.895][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:17.896][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:53:17.903][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:17.904][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:17.905][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-11 18:53:17.906][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:17.907][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.908][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:17.909][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.910][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:17.911][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:17.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:17.913][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:17.914][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:17.915][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:17.916][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:17.917][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.918][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:17.919][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:17.920][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:17.921][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:17.922][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:17.923][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.928][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.DEBUG[2023-04-11 18:53:17.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:17.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:17.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:17.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:17.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:17.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.001][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-11 18:53:18.008][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-11 18:53:18.010][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-11 18:53:18.012][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-11 18:53:18.013][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:53:18.015][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-11 18:53:18.016][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-11 18:53:18.017][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-11 18:53:18.019][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-11 18:53:18.020][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-11 18:53:18.022][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:53:18.023][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-11 18:53:18.024][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-11 18:53:18.026][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-11 18:53:18.027][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-11 18:53:18.028][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:53:18.030][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-11 18:53:18.031][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-11 18:53:18.033][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:53:18.034][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-11 18:53:18.035][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-11 18:53:18.037][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-11 18:53:18.038][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-11 18:53:18.039][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-11 18:53:18.041][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-11 18:53:18.042][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-11 18:53:18.044][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-11 18:53:18.045][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-11 18:53:18.046][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-11 18:53:18.048][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-11 18:53:18.049][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-11 18:53:18.051][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-11 18:53:18.052][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-11 18:53:18.053][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-11 18:53:18.055][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-11 18:53:18.056][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-11 18:53:18.058][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-11 18:53:18.059][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-11 18:53:18.060][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-11 18:53:18.062][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-11 18:53:18.063][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-11 18:53:18.065][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-11 18:53:18.066][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-11 18:53:18.067][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-11 18:53:18.069][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-11 18:53:18.070][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-11 18:53:18.072][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-11 18:53:18.073][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-11 18:53:18.075][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-11 18:53:18.076][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-11 18:53:18.078][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-11 18:53:18.079][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-11 18:53:18.080][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-11 18:53:18.082][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-11 18:53:18.083][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-11 18:53:18.085][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-11 18:53:18.086][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-11 18:53:18.088][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-11 18:53:18.089][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-11 18:53:18.090][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-11 18:53:18.092][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-11 18:53:18.093][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-11 18:53:18.095][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-11 18:53:18.096][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-11 18:53:18.097][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-11 18:53:18.099][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-11 18:53:18.100][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:53:18.101][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:53:18.103][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-11 18:53:18.104][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-11 18:53:18.112][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-11 18:53:18.114][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-11 18:53:18.115][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-11 18:53:18.116][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-11 18:53:18.118][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-11 18:53:18.119][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-11 18:53:18.120][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-11 18:53:18.122][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-11 18:53:18.123][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-11 18:53:18.125][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-11 18:53:18.126][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-11 18:53:18.127][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-11 18:53:18.129][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-11 18:53:18.130][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-11 18:53:18.132][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:53:18.133][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:18.134][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.136][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.155][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[2023-04-11 18:53:18.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.168][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[2023-04-11 18:53:18.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.220][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[2023-04-11 18:53:18.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:18.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:18.255][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-04-11 18:53:18.257][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-04-11 18:53:18.259][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:18.260][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-11 18:53:18.261][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:18.262][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:18.263][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:18.264][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-04-11 18:53:18.265][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:18.266][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:18.267][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-11 18:53:18.268][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:18.269][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:18.270][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-04-11 18:53:18.271][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-04-11 18:53:18.272][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-04-11 18:53:18.274][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:18.274][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:18.274][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-04-11 18:53:18.274][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2023-04-11 18:53:18.276][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-11 18:53:18.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:18.277][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:18.278][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:18.279][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:18.280][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:18.281][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:18.282][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-11 18:53:18.282][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-04-11 18:53:18.283][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:18.284][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:18.285][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:18.286][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:18.287][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2023-04-11 18:53:18.289][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-11 18:53:18.290][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-11 18:53:18.292][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:53:18.293][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:53:18.297][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-04-11 18:53:18.298][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-04-11 18:53:18.299][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-11 18:53:18.301][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-11 18:53:18.302][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:18.303][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:18.304][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-04-11 18:53:18.305][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-04-11 18:53:18.306][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-11 18:53:18.306][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-04-11 18:53:18.307][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:18.308][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:18.309][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-04-11 18:53:18.310][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-04-11 18:53:18.311][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-11 18:53:18.313][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-11 18:53:18.314][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:18.315][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:18.316][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-11 18:53:18.317][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:18.318][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-04-11 18:53:18.326][biodb::testThat]
biodb.INFO [2023-04-11 18:53:18.327][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2023-04-11 18:53:18.328][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:18.329][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:18.333][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:18.335][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:18.336][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-11 18:53:18.338][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:18.339][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-11 18:53:18.343][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-11 18:53:18.345][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-11 18:53:18.346][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-11 18:53:18.347][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-11 18:53:18.349][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2023-04-11 18:53:18.352][biodb::testThat]
biodb.INFO [2023-04-11 18:53:18.354][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2023-04-11 18:53:18.355][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:18.356][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:18.358][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-04-11 18:53:18.359][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-11 18:53:18.361][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:18.363][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-11 18:53:18.365][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-04-11 18:53:18.366][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:18.368][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-04-11 18:53:18.369][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:18.387][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:18.389][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-11 18:53:18.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:18.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:18.404][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.405][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.406][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.407][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.416][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:18.417][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:18.418][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.419][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.420][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:18.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:18.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.433][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:18.435][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:18.436][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.438][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.440][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:18.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:18.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.467][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:18.469][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:18.470][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.471][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.473][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:18.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:18.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.480][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:18.481][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:18.482][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.484][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:18.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:18.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.492][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:18.494][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:18.495][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.496][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:18.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:18.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.505][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:18.506][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:18.507][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.508][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.509][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:18.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:18.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.517][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:18.518][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:18.519][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.520][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.522][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:18.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:18.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.529][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:18.531][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:18.532][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.533][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.534][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:18.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:18.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.541][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:18.543][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:18.544][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.544][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.546][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:18.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:18.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.553][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:18.555][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:18.556][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.557][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.558][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:18.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:18.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.565][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:18.567][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:18.568][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.569][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:18.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:18.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.577][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.578][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.579][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.580][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.594][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:18.596][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:18.597][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.598][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:18.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:18.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.606][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:18.607][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:18.608][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.609][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:18.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:18.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.618][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:18.619][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:18.620][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.622][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.624][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:18.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:18.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.634][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:18.635][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:18.637][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.638][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.639][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:18.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:18.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.646][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-11 18:53:18.647][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:18.648][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.649][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.650][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-11 18:53:18.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:18.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.668][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:18.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:18.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.672][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:18.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:18.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.676][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:18.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:18.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.680][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:18.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:18.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.684][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:18.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:18.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.687][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:18.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:18.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:18.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:18.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:18.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:18.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:18.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:18.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:18.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:18.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:18.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:18.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:18.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:18.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.720][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:18.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:18.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.724][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:18.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:18.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.728][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:18.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:18.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.732][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:18.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:18.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.736][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:18.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:18.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.739][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:18.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:18.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.743][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:18.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:18.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.747][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:18.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:18.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.751][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:18.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:18.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.755][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:18.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:18.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.759][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:18.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:18.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.763][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:18.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:18.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.767][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:18.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:18.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.771][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:18.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:18.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:18.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:18.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.779][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:18.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:18.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:18.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:18.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:18.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:18.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.791][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.808][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:18.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:18.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.812][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:18.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:18.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.816][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:18.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:18.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:18.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:18.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:18.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:18.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:18.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:18.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.833][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:18.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:18.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:18.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:18.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:18.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:18.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.844][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:18.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:18.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.848][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:18.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:18.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.852][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:18.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:18.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.856][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:18.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:18.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.860][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:18.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:18.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.863][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:18.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:18.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.867][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:18.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:18.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.871][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:18.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:18.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.875][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:18.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:18.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.879][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-11 18:53:18.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.894][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-11 18:53:18.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:18.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:18.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:18.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.910][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:18.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:18.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.914][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:18.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:18.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:18.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:18.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:18.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:18.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.929][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:18.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:18.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.933][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:18.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:18.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.940][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:18.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:18.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:18.970][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-04-11 18:53:18.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:18.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:18.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:18.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:18.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:18.985][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-11 18:53:18.986][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-04-11 18:53:18.987][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-04-11 18:53:18.988][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-11 18:53:18.989][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:18.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:18.991][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:18.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:18.992][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:18.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-11 18:53:18.998][biodb::testContext]
biodb.INFO [2023-04-11 18:53:18.998][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:53:18.999][biodb::testContext] Test context - Test search of entries
biodb.INFO [2023-04-11 18:53:19.000][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:53:19.006][biodb::testContext]
biodb.INFO [2023-04-11 18:53:19.013][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:53:19.014][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-11 18:53:19.018][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:19.019][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-11 18:53:19.020][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-11 18:53:19.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.024][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-11 18:53:19.025][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-11 18:53:19.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.028][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-11 18:53:19.029][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-11 18:53:19.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.032][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-11 18:53:19.033][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-11 18:53:19.034][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-11 18:53:19.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.038][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-11 18:53:19.039][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-11 18:53:19.040][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-11 18:53:19.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.043][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-11 18:53:19.044][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-11 18:53:19.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.048][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-11 18:53:19.049][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-11 18:53:19.050][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-11 18:53:19.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.053][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-11 18:53:19.054][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-11 18:53:19.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.057][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-11 18:53:19.058][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-11 18:53:19.059][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-11 18:53:19.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.063][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:53:19.064][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-11 18:53:19.065][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-11 18:53:19.065][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-11 18:53:19.066][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-11 18:53:19.067][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-11 18:53:19.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.071][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-11 18:53:19.072][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-11 18:53:19.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.074][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[2023-04-11 18:53:19.075][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-11 18:53:19.076][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-11 18:53:19.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.080][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-11 18:53:19.081][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-11 18:53:19.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.084][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-11 18:53:19.085][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-11 18:53:19.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.089][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-11 18:53:19.090][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-11 18:53:19.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.093][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:53:19.094][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-11 18:53:19.097][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-11 18:53:19.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.100][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-11 18:53:19.101][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-11 18:53:19.107][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-11 18:53:19.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.111][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-11 18:53:19.113][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.114][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-11 18:53:19.115][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.116][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:19.117][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.118][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.119][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.120][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.121][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:53:19.122][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:19.123][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.124][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-11 18:53:19.124][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:19.125][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.126][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.127][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:19.127][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:53:19.127][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:53:19.127][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:53:19.127][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:53:19.128][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:19.129][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:19.130][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:19.131][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:19.132][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:19.133][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:19.134][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.135][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.136][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:19.136][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:19.137][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.138][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.139][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-11 18:53:19.141][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.142][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:53:19.143][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.144][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:19.145][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.146][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.147][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.148][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.148][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:53:19.149][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:19.150][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.151][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-11 18:53:19.152][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:19.153][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.154][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.155][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:19.155][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:53:19.155][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:53:19.155][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:53:19.155][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:53:19.156][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:19.157][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:19.158][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:19.159][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:19.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:19.160][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:19.161][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.162][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.163][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:19.164][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:19.165][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.166][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.167][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-11 18:53:19.169][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.170][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-11 18:53:19.171][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.172][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:19.172][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.173][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.174][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.175][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.176][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:53:19.177][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:19.178][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.179][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-11 18:53:19.180][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:19.181][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.182][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.183][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.184][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:19.185][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:19.185][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:19.186][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:19.187][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:19.188][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:19.189][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.190][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.191][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:19.192][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:19.193][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.194][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.195][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-11 18:53:19.196][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.197][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:53:19.203][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.204][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:19.205][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.206][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.207][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.208][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.209][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:53:19.210][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:19.211][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.212][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-11 18:53:19.213][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:19.214][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.215][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.216][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.217][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:19.218][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:19.219][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:19.220][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:19.221][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:19.221][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:19.222][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.223][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.224][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:19.225][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:19.226][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.227][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.228][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:19.229][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.230][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[2023-04-11 18:53:19.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.243][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[2023-04-11 18:53:19.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.256][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[2023-04-11 18:53:19.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.277][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[2023-04-11 18:53:19.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.285][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[2023-04-11 18:53:19.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.308][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-11 18:53:19.309][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-11 18:53:19.311][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-11 18:53:19.312][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-11 18:53:19.313][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:53:19.315][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-11 18:53:19.316][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-11 18:53:19.317][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-11 18:53:19.319][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-11 18:53:19.320][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-11 18:53:19.321][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:53:19.323][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-11 18:53:19.324][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-11 18:53:19.325][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-11 18:53:19.327][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-11 18:53:19.328][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:53:19.329][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-11 18:53:19.331][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-11 18:53:19.332][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:53:19.333][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-11 18:53:19.335][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-11 18:53:19.336][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-11 18:53:19.337][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-11 18:53:19.339][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-11 18:53:19.340][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-11 18:53:19.341][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-11 18:53:19.342][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-11 18:53:19.344][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-11 18:53:19.345][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-11 18:53:19.346][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-11 18:53:19.348][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-11 18:53:19.349][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-11 18:53:19.350][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-11 18:53:19.352][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-11 18:53:19.353][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-11 18:53:19.354][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-11 18:53:19.355][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-11 18:53:19.357][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-11 18:53:19.358][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-11 18:53:19.359][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-11 18:53:19.361][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-11 18:53:19.362][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-11 18:53:19.363][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-11 18:53:19.365][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-11 18:53:19.366][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-11 18:53:19.367][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-11 18:53:19.368][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-11 18:53:19.370][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-11 18:53:19.371][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-11 18:53:19.372][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-11 18:53:19.374][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-11 18:53:19.375][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-11 18:53:19.376][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-11 18:53:19.378][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-11 18:53:19.379][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-11 18:53:19.380][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-11 18:53:19.381][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-11 18:53:19.383][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-11 18:53:19.384][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-11 18:53:19.409][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-11 18:53:19.411][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-11 18:53:19.413][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-11 18:53:19.415][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-11 18:53:19.416][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-11 18:53:19.418][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-11 18:53:19.419][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-11 18:53:19.421][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:53:19.422][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:53:19.423][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-11 18:53:19.424][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-11 18:53:19.426][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-11 18:53:19.427][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-11 18:53:19.428][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-11 18:53:19.430][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-11 18:53:19.431][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-11 18:53:19.432][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-11 18:53:19.434][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-11 18:53:19.435][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-11 18:53:19.436][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-11 18:53:19.438][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-11 18:53:19.439][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-11 18:53:19.440][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-11 18:53:19.442][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-11 18:53:19.443][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-11 18:53:19.445][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:53:19.446][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:19.446][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.448][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.491][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[2023-04-11 18:53:19.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.497][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[2023-04-11 18:53:19.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:19.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:19.558][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-04-11 18:53:19.559][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-04-11 18:53:19.561][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.562][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.563][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.564][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:19.565][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.566][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-04-11 18:53:19.567][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.568][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.569][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-11 18:53:19.570][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:19.570][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.571][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-04-11 18:53:19.572][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-04-11 18:53:19.573][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-04-11 18:53:19.575][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:19.576][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:19.576][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-04-11 18:53:19.576][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2023-04-11 18:53:19.577][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-11 18:53:19.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:19.578][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:19.579][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:19.580][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:19.581][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:19.582][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:19.583][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-11 18:53:19.583][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-04-11 18:53:19.584][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:19.585][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:19.586][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:19.586][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:19.588][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2023-04-11 18:53:19.589][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-11 18:53:19.591][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-11 18:53:19.592][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:53:19.594][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:53:19.597][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-04-11 18:53:19.598][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-04-11 18:53:19.599][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-11 18:53:19.600][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-11 18:53:19.601][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:19.602][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:19.603][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-04-11 18:53:19.609][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-04-11 18:53:19.611][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-11 18:53:19.611][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-04-11 18:53:19.612][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:19.613][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:19.614][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-04-11 18:53:19.615][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-04-11 18:53:19.616][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-11 18:53:19.618][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-11 18:53:19.619][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:19.620][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:19.621][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-11 18:53:19.622][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-11 18:53:19.623][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-04-11 18:53:19.625][biodb::testThat]
biodb.INFO [2023-04-11 18:53:19.626][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2023-04-11 18:53:19.626][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:19.627][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:19.637][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-04-11 18:53:19.639][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2023-04-11 18:53:19.639][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2023-04-11 18:53:19.643][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:19.644][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:19.645][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-11 18:53:19.647][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:19.648][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-11 18:53:19.652][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-11 18:53:19.653][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-11 18:53:19.654][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-11 18:53:19.655][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-11 18:53:19.656][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-11 18:53:19.657][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2023-04-11 18:53:19.659][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-04-11 18:53:19.660][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-11 18:53:19.661][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:19.663][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-11 18:53:19.664][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-04-11 18:53:19.666][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:19.668][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-04-11 18:53:19.669][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:19.686][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:19.687][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-11 18:53:19.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:19.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:19.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:19.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:19.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:19.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:19.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:19.703][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.704][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.705][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.706][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.714][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:19.715][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:19.721][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.723][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.724][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:19.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:19.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.732][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:19.733][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:19.734][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.735][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.736][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:19.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:19.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.743][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:19.744][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:19.745][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.746][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.747][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:19.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:19.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.754][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.755][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.756][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.756][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.765][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:19.766][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:19.766][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.767][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:19.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:19.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.775][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:19.776][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:19.777][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.778][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.779][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:19.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:19.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.786][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:19.787][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:19.788][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.789][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.790][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:19.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:19.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.797][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:19.798][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:19.799][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.800][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.801][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:19.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:19.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.808][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:19.809][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:19.810][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.811][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.812][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:19.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:19.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.819][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:19.820][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:19.821][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.822][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.823][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:19.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:19.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.835][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:19.836][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:19.838][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.839][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.840][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:19.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:19.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.847][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:19.848][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:19.849][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.849][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:19.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:19.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.858][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:19.859][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:19.860][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.861][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:19.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:19.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.870][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:19.871][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:19.872][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.873][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.874][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:19.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:19.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.881][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:19.882][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:19.883][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.884][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.885][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:19.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:19.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.892][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:19.893][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:19.894][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.895][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.896][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:19.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:19.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.903][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-11 18:53:19.904][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:19.905][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.906][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.908][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-11 18:53:19.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:19.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:19.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:19.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.926][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:19.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:19.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.930][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:19.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:19.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.933][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:19.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:19.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.942][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:19.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:19.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.947][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:19.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:19.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.951][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:19.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:19.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:19.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:19.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:19.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:19.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:19.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:19.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:19.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.978][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:19.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:19.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.982][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:19.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:19.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.985][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:19.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:19.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.989][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:19.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:19.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:19.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:19.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:19.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:19.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.001][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:20.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:20.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.005][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.010][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.014][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.018][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.023][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.027][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.031][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:20.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:20.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.035][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:20.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:20.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.040][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:20.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:20.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:20.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:20.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:20.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:20.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.071][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:20.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:20.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.080][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.084][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.088][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.092][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.096][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.117][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.124][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.128][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.132][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.136][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.140][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.144][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.147][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:20.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:20.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.151][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:20.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:20.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.155][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:20.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:20.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.159][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-11 18:53:20.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.172][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.181][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-11 18:53:20.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.193][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.205][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.212][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:20.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:20.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.216][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:20.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:20.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.224][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:20.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:20.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:20.255][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-04-11 18:53:20.256][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.260][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.264][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.268][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:20.278][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-11 18:53:20.279][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-11 18:53:20.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:20.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:20.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:20.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:20.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:20.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:20.292][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[2023-04-11 18:53:20.293][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-04-11 18:53:20.294][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-11 18:53:20.296][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:20.298][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-11 18:53:20.300][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-04-11 18:53:20.301][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:20.302][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-04-11 18:53:20.303][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:20.321][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:20.322][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-11 18:53:20.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:20.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:20.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:20.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:20.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:20.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:20.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:20.337][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.338][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.339][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.340][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.348][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.349][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.350][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.351][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.352][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.359][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:20.360][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:20.361][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.362][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.363][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:20.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:20.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.370][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:20.371][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:20.372][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.372][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.374][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:20.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:20.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.381][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:20.388][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:20.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.390][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:20.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:20.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.400][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:20.401][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:20.402][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.403][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:20.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:20.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.412][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.413][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.414][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.415][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.416][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.423][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.425][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.426][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.427][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.428][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.435][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:20.436][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:20.437][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.438][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.440][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:20.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:20.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.446][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:20.447][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:20.448][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.449][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.451][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:20.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:20.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.457][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:20.458][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:20.459][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.460][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.461][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:20.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:20.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.468][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:20.469][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:20.470][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.471][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.472][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:20.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:20.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.479][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.480][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.481][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.482][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.483][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.490][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.491][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.492][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.493][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.507][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.508][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.509][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.510][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.512][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.518][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.519][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.520][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.521][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.523][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.529][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:20.530][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:20.531][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.532][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.533][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:20.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:20.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.540][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-11 18:53:20.541][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.542][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.543][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.544][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-11 18:53:20.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.563][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:20.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:20.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.567][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:20.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:20.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.571][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:20.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:20.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.575][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:20.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:20.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.578][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:20.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:20.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.582][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-11 18:53:20.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-11 18:53:20.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:20.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:20.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:20.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:20.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:20.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:20.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:20.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:20.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:20.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:20.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:20.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-11 18:53:20.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.616][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:20.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:20.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.620][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:20.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:20.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.624][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:20.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:20.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.628][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:20.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:20.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.632][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:20.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:20.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.636][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:20.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-11 18:53:20.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.640][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.644][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.648][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-11 18:53:20.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.652][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.656][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.660][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.664][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:20.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:20.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.668][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:20.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:20.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.671][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:20.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:20.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:20.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:20.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:20.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:20.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-11 18:53:20.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-11 18:53:20.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.699][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.702][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.711][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:20.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:20.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.728][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.736][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.739][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.743][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.747][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:20.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.751][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.755][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.759][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-11 18:53:20.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.763][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:20.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:20.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.766][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:20.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:20.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.770][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-11 18:53:20.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-11 18:53:20.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.774][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-11 18:53:20.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.790][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-11 18:53:20.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-11 18:53:20.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.798][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.802][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:20.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:20.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.827][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:20.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:20.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.831][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:20.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:20.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.839][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:20.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:20.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:20.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:20.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:20.870][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-04-11 18:53:20.871][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.875][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.878][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.882][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:20.886][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-11 18:53:20.887][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2023-04-11 18:53:20.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:20.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:20.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:20.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:20.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:20.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:20.899][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[2023-04-11 18:53:20.911][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-04-11 18:53:20.912][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-04-11 18:53:20.913][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-04-11 18:53:20.920][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:20.921][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:20.923][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-11 18:53:20.925][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:20.926][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-11 18:53:20.930][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-11 18:53:20.931][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-11 18:53:20.932][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-11 18:53:20.933][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-11 18:53:20.934][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-11 18:53:20.935][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-11 18:53:20.937][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.941][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.945][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.949][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.953][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.956][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.960][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:20.964][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-11 18:53:20.965][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-11 18:53:20.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:20.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:20.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:20.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:20.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:20.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:20.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:20.977][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.981][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.985][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.989][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.993][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:20.996][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:20.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:20.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:20.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.000][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:21.004][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-04-11 18:53:21.005][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-11 18:53:21.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:21.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:21.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:21.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:21.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:21.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:21.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:21.033][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-04-11 18:53:21.034][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-04-11 18:53:21.035][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-04-11 18:53:21.036][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:21.038][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:21.039][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-11 18:53:21.041][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-11 18:53:21.041][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-11 18:53:21.046][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-11 18:53:21.047][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-11 18:53:21.048][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-11 18:53:21.048][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-11 18:53:21.049][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-11 18:53:21.050][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-11 18:53:21.052][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.056][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.060][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.064][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.068][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.072][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.076][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:21.080][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-04-11 18:53:21.081][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2023-04-11 18:53:21.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:21.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:21.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:21.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:21.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:21.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:21.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:21.093][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.097][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.101][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.105][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.109][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.113][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:21.117][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-11 18:53:21.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-11 18:53:21.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:21.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:21.120][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-11 18:53:21.121][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-11 18:53:21.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:21.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:21.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:21.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:21.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:21.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:21.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-11 18:53:21.143][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-11 18:53:21.144][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-04-11 18:53:21.145][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-04-11 18:53:21.146][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-11 18:53:21.147][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:21.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:21.149][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:21.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:21.151][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:21.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 199 ]
>
> proc.time()
user system elapsed
9.649 0.467 11.333
biodbHmdb.Rcheck/biodbHmdb-Ex.timings
| name | user | system | elapsed | |
| HmdbMetabolitesConn | 0.528 | 0.044 | 0.572 | |
| HmdbMetabolitesEntry | 0.112 | 0.016 | 0.127 | |