| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:34 -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: 2023-04-12 04:58:06 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 04:59:08 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 61.2 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 Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 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 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* checking installed package size ... NOTE
installed size is 10.1Mb
sub-directories of 1Mb or more:
libs 9.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘biodbHmdb.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-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 9.4.0-1ubuntu1~20.04.1) 9.4.0’ 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 Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
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 [2023-04-12 04:58:50.522][biodb::testContext]
biodb.INFO [2023-04-12 04:58:50.525][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:58:50.526][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2023-04-12 04:58:50.527][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:58:50.528][biodb::testContext]
biodb.INFO [2023-04-12 04:58:50.530][biodb::testThat]
biodb.INFO [2023-04-12 04:58:50.531][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2023-04-12 04:58:50.532][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:50.533][biodb::testThat]
biodb.INFO [2023-04-12 04:58:50.632][biodb::testContext]
biodb.INFO [2023-04-12 04:58:50.633][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:58:50.634][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-04-12 04:58:50.635][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:58:50.636][biodb::testContext]
biodb.INFO [2023-04-12 04:58:50.654][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:58:50.656][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-12 04:58:50.664][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:50.665][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-12 04:58:50.667][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-12 04:58:50.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.670][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-12 04:58:50.690][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-12 04:58:50.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.695][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-12 04:58:50.696][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-12 04:58:50.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.700][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-12 04:58:50.701][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-12 04:58:50.702][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-12 04:58:50.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.706][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-12 04:58:50.707][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-12 04:58:50.708][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-12 04:58:50.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.721][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-12 04:58:50.722][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-12 04:58:50.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.725][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[2023-04-12 04:58:50.726][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-12 04:58:50.727][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-12 04:58:50.728][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-12 04:58:50.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.731][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-12 04:58:50.732][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-12 04:58:50.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.736][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-12 04:58:50.737][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-12 04:58:50.738][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-12 04:58:50.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.741][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:58:50.742][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-12 04:58:50.743][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-12 04:58:50.744][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-12 04:58:50.745][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-12 04:58:50.746][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-12 04:58:50.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.750][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-12 04:58:50.750][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-12 04:58:50.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.754][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-12 04:58:50.755][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-12 04:58:50.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.758][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-12 04:58:50.759][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-12 04:58:50.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.763][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-12 04:58:50.764][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-12 04:58:50.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.767][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-12 04:58:50.768][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-12 04:58:50.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.772][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:58:50.773][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-12 04:58:50.777][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-12 04:58:50.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.781][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-12 04:58:50.782][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-12 04:58:50.783][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-12 04:58:50.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.790][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-12 04:58:50.825][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:50.840][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-12 04:58:50.842][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.843][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:50.844][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.845][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:50.846][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:50.847][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:50.848][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:58:50.849][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:50.850][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.850][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-12 04:58:50.851][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:50.852][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.853][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.854][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:50.854][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:58:50.854][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:58:50.854][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:58:50.854][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:58:50.855][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:50.856][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:50.857][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:50.858][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:50.859][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:50.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:50.860][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:50.861][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.862][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:50.863][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:50.864][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:50.865][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.866][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-12 04:58:50.868][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:50.869][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:58:50.870][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.870][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:50.871][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.872][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:50.873][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:50.874][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:50.875][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:58:50.876][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:50.877][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.884][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-12 04:58:50.885][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:50.886][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.887][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.888][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:50.888][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:58:50.888][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:58:50.888][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:58:50.888][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:58:50.888][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:50.889][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:50.890][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:50.891][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:50.892][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:50.893][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:50.894][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:50.895][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.895][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:50.896][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:50.897][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:50.898][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.899][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-12 04:58:50.901][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.902][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-12 04:58:50.903][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.904][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:50.904][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.905][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:50.906][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:50.907][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:50.908][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:58:50.909][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:50.910][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:50.911][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-12 04:58:50.912][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:50.913][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.914][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.915][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.916][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:50.917][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:50.918][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:50.918][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:50.919][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:50.920][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:50.921][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:50.922][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.923][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:50.924][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:50.925][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:50.925][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.927][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-12 04:58:50.928][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.929][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:58:50.930][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.931][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:50.932][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.933][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:50.934][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:50.935][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:50.936][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:58:50.937][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:50.938][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:50.939][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-12 04:58:50.940][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:50.941][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.942][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:50.943][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.944][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:50.944][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:50.945][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:50.946][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:50.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:50.948][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:50.949][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:50.950][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.951][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:50.951][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:50.952][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:50.953][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:50.957][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:50.958][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.959][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[2023-04-12 04:58:50.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:50.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:50.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:50.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:50.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.968][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[2023-04-12 04:58:50.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:50.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:50.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:50.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:50.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.976][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.DEBUG[2023-04-12 04:58:50.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:50.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:50.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:50.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:50.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:50.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:50.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:50.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:50.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:50.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:50.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:50.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:50.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:50.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:50.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.031][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-12 04:58:51.042][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-12 04:58:51.044][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-12 04:58:51.046][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-12 04:58:51.047][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 04:58:51.049][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-12 04:58:51.050][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-12 04:58:51.051][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-12 04:58:51.053][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-12 04:58:51.054][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-12 04:58:51.055][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:58:51.057][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-12 04:58:51.058][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-12 04:58:51.059][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-12 04:58:51.061][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-12 04:58:51.062][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 04:58:51.063][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-12 04:58:51.065][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-12 04:58:51.066][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 04:58:51.067][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-12 04:58:51.069][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-12 04:58:51.070][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-12 04:58:51.071][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-12 04:58:51.073][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-12 04:58:51.074][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-12 04:58:51.076][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-12 04:58:51.077][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-12 04:58:51.078][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-12 04:58:51.080][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-12 04:58:51.081][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-12 04:58:51.083][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-12 04:58:51.084][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-12 04:58:51.085][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-12 04:58:51.087][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-12 04:58:51.088][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-12 04:58:51.089][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-12 04:58:51.090][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-12 04:58:51.092][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-12 04:58:51.093][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-12 04:58:51.094][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-12 04:58:51.096][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-12 04:58:51.097][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-12 04:58:51.098][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-12 04:58:51.100][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-12 04:58:51.101][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-12 04:58:51.102][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-12 04:58:51.104][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-12 04:58:51.105][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-12 04:58:51.106][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-12 04:58:51.107][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-12 04:58:51.109][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-12 04:58:51.110][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-12 04:58:51.111][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-12 04:58:51.113][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-12 04:58:51.114][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-12 04:58:51.115][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-12 04:58:51.116][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-12 04:58:51.118][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-12 04:58:51.119][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-12 04:58:51.120][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-12 04:58:51.122][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-12 04:58:51.123][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-12 04:58:51.124][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-12 04:58:51.125][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-12 04:58:51.127][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-12 04:58:51.128][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-12 04:58:51.129][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 04:58:51.131][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 04:58:51.132][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-12 04:58:51.133][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-12 04:58:51.135][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-12 04:58:51.136][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-12 04:58:51.138][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-12 04:58:51.139][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-12 04:58:51.140][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-12 04:58:51.142][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-12 04:58:51.143][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-12 04:58:51.144][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-12 04:58:51.146][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-12 04:58:51.147][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-12 04:58:51.148][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-12 04:58:51.150][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-12 04:58:51.151][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-12 04:58:51.157][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-12 04:58:51.159][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:58:51.162][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:51.163][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.165][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.256][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[2023-04-12 04:58:51.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.268][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[2023-04-12 04:58:51.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.292][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[2023-04-12 04:58:51.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.298][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[2023-04-12 04:58:51.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:51.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:51.312][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-04-12 04:58:51.321][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-04-12 04:58:51.323][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:51.325][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-12 04:58:51.326][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:51.327][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:51.328][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:51.329][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-04-12 04:58:51.330][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:51.331][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:51.332][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-12 04:58:51.333][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:51.334][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:51.335][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-04-12 04:58:51.336][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-04-12 04:58:51.337][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-04-12 04:58:51.338][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:51.339][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:51.339][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-04-12 04:58:51.339][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2023-04-12 04:58:51.340][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-12 04:58:51.341][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:51.342][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:51.343][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:51.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:51.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:51.345][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:51.346][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-12 04:58:51.346][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-04-12 04:58:51.347][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:51.348][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:51.349][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:51.350][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:51.356][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2023-04-12 04:58:51.357][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-12 04:58:51.359][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-12 04:58:51.360][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:58:51.362][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 04:58:51.394][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-04-12 04:58:51.395][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-04-12 04:58:51.400][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-12 04:58:51.405][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-12 04:58:51.409][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:51.411][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:51.412][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-04-12 04:58:51.413][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-04-12 04:58:51.414][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-12 04:58:51.414][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-04-12 04:58:51.415][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:51.416][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:51.417][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-04-12 04:58:51.418][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-04-12 04:58:51.419][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-12 04:58:51.435][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-12 04:58:51.437][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:51.438][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:51.439][private$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[2023-04-12 04:58:51.441][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:51.442][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-04-12 04:58:51.458][biodb::testThat]
biodb.INFO [2023-04-12 04:58:51.459][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-04-12 04:58:51.460][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:51.461][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:51.466][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[2023-04-12 04:58:51.471][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:51.475][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-12 04:58:51.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:51.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:51.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:51.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:51.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:51.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:51.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:51.505][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:51.506][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:51.507][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.508][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:51.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:51.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.528][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:51.529][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:51.530][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.531][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.566][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:51.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:51.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.574][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:51.575][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:51.576][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.577][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.579][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:51.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:51.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.586][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:51.587][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:51.588][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.589][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.590][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:51.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:51.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.597][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:51.598][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:51.599][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.600][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:51.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:51.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.608][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:51.609][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:51.610][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.611][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:51.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:51.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.619][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:51.620][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:51.621][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.622][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.623][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:51.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:51.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.634][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:51.635][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:51.636][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.637][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.638][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:51.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:51.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.645][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:51.646][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:51.647][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.648][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.650][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:51.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:51.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.657][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:51.658][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:51.659][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.660][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.662][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:51.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:51.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.669][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:51.670][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:51.671][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.672][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.673][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:51.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:51.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.680][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:51.682][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:51.683][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.684][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:51.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:51.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.692][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:51.693][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:51.694][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.695][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.697][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:51.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:51.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.710][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:51.711][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:51.712][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.712][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:51.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:51.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.721][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:51.722][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:51.723][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.724][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:51.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:51.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.732][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:51.733][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:51.734][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.735][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.736][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:51.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:51.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.743][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:51.744][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:51.745][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.746][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.748][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:51.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:51.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.755][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-12 04:58:51.756][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:51.757][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.758][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.759][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-12 04:58:51.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:51.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:51.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:51.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:51.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:51.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:51.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:51.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.811][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:51.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:51.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.816][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:51.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:51.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.820][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:51.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:51.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.823][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:51.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:51.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.832][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:51.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:51.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.836][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:51.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:51.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:51.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:51.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:51.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:51.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:51.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:51.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:51.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:51.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:51.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:51.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:51.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:51.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.862][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:51.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:51.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.866][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:51.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:51.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.870][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:51.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:51.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.874][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:51.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:51.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.877][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:51.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:51.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.881][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:51.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:51.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.885][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:51.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:51.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.889][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:51.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:51.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.892][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:51.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:51.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.896][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:51.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:51.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.900][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:51.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:51.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.904][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:51.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:51.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.907][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:51.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:51.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.911][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:51.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:51.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.915][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:51.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:51.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:51.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:51.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:51.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:51.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.926][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:51.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:51.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:51.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:51.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.934][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:51.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:51.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.938][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:51.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:51.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.941][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:51.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:51.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.945][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:51.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:51.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.949][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:51.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:51.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:51.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:51.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:51.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:51.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:51.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:51.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.969][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:51.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:51.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:51.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:51.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.977][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:51.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:51.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.981][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:51.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:51.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.985][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:51.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:51.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.989][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:51.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:51.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.992][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:51.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:51.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:51.996][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:51.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:51.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:51.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.000][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.004][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:52.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:52.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.008][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:52.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:52.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.012][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:52.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:52.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.016][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-12 04:58:52.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.020][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.027][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.031][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-12 04:58:52.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.054][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:52.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:52.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.058][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:52.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:52.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.062][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:52.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:52.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:52.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:52.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.069][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:52.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:52.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.082][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.087][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.094][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:52.125][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2023-04-12 04:58:52.130][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:52.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:52.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.134][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:52.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:52.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.138][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:52.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:52.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.142][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:52.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:52.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.169][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.201][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.205][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.214][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:52.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.238][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.240][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.240][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.241][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.254][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.259][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.263][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.267][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.268][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.269][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.270][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.271][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:52.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:52.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:52.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:52.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:52.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:52.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.296][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:52.297][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:52.298][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.299][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:52.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:52.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.313][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:52.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:52.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.318][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:52.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:52.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.322][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:52.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:52.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.326][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:52.327][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:52.328][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.329][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.330][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:52.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:52.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.362][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.364][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.365][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.366][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.379][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:52.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:52.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.384][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:52.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:52.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.388][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:52.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:52.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.392][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:52.393][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:52.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.395][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.397][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:52.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:52.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:52.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:52.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:52.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:52.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.417][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:52.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:52.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.422][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:52.423][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:52.424][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.425][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:52.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:52.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.437][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:52.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:52.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.441][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:52.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:52.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.445][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:52.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:52.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.449][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:52.450][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:52.451][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.452][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.453][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:52.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:52.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.464][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:52.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:52.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.469][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:52.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:52.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.473][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:52.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:52.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.477][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:52.478][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:52.479][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.480][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.481][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:52.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:52.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.498][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:52.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:52.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.502][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:52.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:52.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.506][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:52.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:52.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.510][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:52.511][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:52.512][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.513][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.514][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:52.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:52.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:52.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:52.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:52.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:52.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:52.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:52.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.539][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:52.540][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:52.541][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.542][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:52.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:52.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.555][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:52.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:52.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.560][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:52.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:52.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.564][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:52.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:52.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.568][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:52.570][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:52.571][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.572][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.573][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:52.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:52.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.585][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:52.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:52.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.590][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:52.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:52.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.594][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:52.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:52.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.599][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:52.600][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:52.601][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.602][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.603][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:52.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:52.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.616][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:52.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:52.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.621][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:52.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:52.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.625][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:52.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:52.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.637][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:52.638][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:52.639][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.640][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.641][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:52.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:52.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.653][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:52.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:52.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.658][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:52.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:52.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.662][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:52.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:52.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.666][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:52.667][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:52.669][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.670][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.671][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:52.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:52.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:52.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:52.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:52.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:52.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:52.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:52.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.695][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:52.696][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:52.697][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.698][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.699][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:52.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:52.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.714][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.721][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.722][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.723][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.724][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.725][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.736][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:52.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:52.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.740][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:52.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:52.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.744][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:52.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:52.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.748][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:52.749][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:52.750][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.751][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.752][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:52.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:52.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.763][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:52.764][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:52.771][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.772][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.778][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:52.779][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:52.780][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.781][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.787][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:52.788][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:52.789][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.790][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.796][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.797][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:52.798][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.799][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.804][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:52.806][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:52.807][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.808][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.813][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:52.814][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:52.815][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.816][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.822][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:52.823][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:52.824][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.825][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.831][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:52.832][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:52.833][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.834][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.839][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:52.840][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:52.841][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.842][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.847][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:52.848][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:52.849][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.850][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.855][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:52.856][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:52.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.858][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.863][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.864][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:52.865][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.866][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.871][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:52.872][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:52.873][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.874][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.879][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:52.880][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:52.881][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.882][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.887][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:52.888][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:52.889][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.890][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.900][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:52.901][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:52.902][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.903][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.908][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.909][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:52.910][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.911][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:52.916][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:52.917][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:52.918][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:52.919][ef$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:52.925][biodb::testThat]
biodb.INFO [2023-04-12 04:58:52.926][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-12 04:58:52.927][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:52.928][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:52.941][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-04-12 04:58:52.949][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-12 04:58:52.954][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:52.956][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-12 04:58:52.958][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-04-12 04:58:52.959][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:52.962][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-04-12 04:58:52.963][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:53.005][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:53.006][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-12 04:58:53.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:53.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:53.031][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.033][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.033][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.034][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.042][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.043][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.044][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.045][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.047][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.054][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:53.055][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:53.056][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.057][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.058][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:53.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:53.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.065][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:53.067][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:53.068][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.068][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.070][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:53.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:53.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.077][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.078][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.079][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.080][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.089][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:53.090][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:53.091][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.092][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:53.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:53.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.101][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.102][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.103][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.104][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.105][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.112][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.114][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.114][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.115][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.117][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.124][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.125][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.126][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.127][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.129][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.136][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:53.137][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:53.138][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.139][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.140][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:53.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:53.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.147][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:53.149][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:53.150][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.151][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.152][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:53.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:53.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.167][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:53.168][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:53.169][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.170][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.172][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:53.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:53.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.180][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.181][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.182][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.183][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.185][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.193][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.194][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.195][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.196][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.206][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.208][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.209][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.210][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.211][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.219][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:53.220][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:53.221][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.222][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.223][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:53.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:53.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.231][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:53.233][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:53.234][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.235][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.237][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:53.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:53.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.245][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-12 04:58:53.246][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:53.247][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.248][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.250][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-12 04:58:53.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:53.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.271][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:53.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:53.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.275][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:53.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:53.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.279][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:53.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:53.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.283][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:53.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:53.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.287][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:53.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:53.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.291][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:53.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:53.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:53.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:53.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:53.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:53.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:53.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:53.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.327][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.331][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.335][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.339][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:53.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:53.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.343][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:53.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:53.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.347][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:53.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:53.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.351][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:53.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:53.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.355][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:53.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:53.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.359][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:53.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:53.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.363][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:53.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:53.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.367][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:53.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:53.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.371][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:53.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:53.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.375][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:53.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:53.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.379][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:53.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:53.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.383][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:53.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:53.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.387][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:53.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:53.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:53.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:53.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:53.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:53.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.398][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.410][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.414][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.418][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.443][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.447][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.451][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.455][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.459][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.463][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.467][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.470][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.474][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:53.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:53.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.478][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:53.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:53.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.482][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:53.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:53.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.486][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-12 04:58:53.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.490][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.502][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-12 04:58:53.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:53.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.526][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.533][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:53.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:53.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.537][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:53.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:53.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.544][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:53.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:53.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:53.579][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-04-12 04:58:53.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-12 04:58:53.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-12 04:58:53.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-12 04:58:53.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-12 04:58:53.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-12 04:58:53.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-12 04:58:53.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:53.598][biodb::testThat]
biodb.INFO [2023-04-12 04:58:53.599][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-12 04:58:53.600][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:53.601][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:53.604][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.605][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.606][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.607][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:53.608][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2023-04-12 04:58:53.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.641][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:53.651][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2023-04-12 04:58:53.661][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-04-12 04:58:53.662][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-04-12 04:58:53.663][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-04-12 04:58:53.665][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:53.667][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:53.668][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-12 04:58:53.669][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:53.670][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-12 04:58:53.682][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-12 04:58:53.684][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-12 04:58:53.685][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-12 04:58:53.686][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-12 04:58:53.687][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-12 04:58:53.688][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-12 04:58:53.690][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:53.706][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-12 04:58:53.706][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-12 04:58:53.707][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2023-04-12 04:58:53.722][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:53.723][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:53.724][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.725][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:53.726][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2023-04-12 04:58:53.741][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:53.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:53.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.745][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:53.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:53.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.749][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:53.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:53.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:53.754][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[2023-04-12 04:58:53.820][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-04-12 04:58:53.822][private$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[2023-04-12 04:58:53.823][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2023-04-12 04:58:53.837][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:53.839][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:53.840][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-12 04:58:53.842][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:53.843][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-12 04:58:53.862][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-12 04:58:53.864][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-12 04:58:53.865][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-12 04:58:53.866][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-12 04:58:53.867][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-12 04:58:53.868][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-12 04:58:53.870][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:53.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:53.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.874][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:53.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:53.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.878][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:53.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:53.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.882][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:53.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:53.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:53.886][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-12 04:58:53.887][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-12 04:58:53.888][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2023-04-12 04:58:53.907][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.908][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.909][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.910][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:53.911][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2023-04-12 04:58:53.925][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.929][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.933][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:53.939][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2023-04-12 04:58:53.949][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2023-04-12 04:58:53.950][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2023-04-12 04:58:53.951][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2023-04-12 04:58:53.953][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:53.955][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:53.956][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-12 04:58:53.958][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:53.959][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-12 04:58:53.963][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-12 04:58:53.964][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-12 04:58:53.965][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-12 04:58:53.966][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-12 04:58:53.968][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-12 04:58:53.968][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-12 04:58:53.970][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.974][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.978][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.982][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:53.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:53.986][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-12 04:58:53.987][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-12 04:58:53.988][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2023-04-12 04:58:54.004][biodb::testThat]
biodb.INFO [2023-04-12 04:58:54.005][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-04-12 04:58:54.006][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:54.007][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:54.025][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:54.078][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2023-04-12 04:58:54.079][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-04-12 04:58:54.080][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2023-04-12 04:58:54.082][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:54.083][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:54.085][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-12 04:58:54.086][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:54.087][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-12 04:58:54.092][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-12 04:58:54.093][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-12 04:58:54.094][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-12 04:58:54.095][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-12 04:58:54.096][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-12 04:58:54.097][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-12 04:58:54.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.106][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.110][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:54.114][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-12 04:58:54.115][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2023-04-12 04:58:54.129][biodb::testThat]
biodb.INFO [2023-04-12 04:58:54.131][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-04-12 04:58:54.132][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:54.133][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:54.159][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:54.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:54.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.163][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:54.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:54.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.166][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:54.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:54.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.170][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:54.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:54.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.221][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:54.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:54.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.225][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:54.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:54.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.229][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:54.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:54.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.233][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:54.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:54.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:54.239][biodb::testThat]
biodb.INFO [2023-04-12 04:58:54.240][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-12 04:58:54.241][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:54.242][biodb::testThat]
biodb.INFO [2023-04-12 04:58:54.247][biodb::testThat]
biodb.INFO [2023-04-12 04:58:54.248][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-12 04:58:54.249][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:54.250][biodb::testThat]
biodb.INFO [2023-04-12 04:58:54.255][biodb::testThat]
biodb.INFO [2023-04-12 04:58:54.256][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-12 04:58:54.257][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:54.258][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:54.261][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2023-04-12 04:58:55.303][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2023-04-12 04:58:55.416][biodb::testThat]
biodb.INFO [2023-04-12 04:58:55.418][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-12 04:58:55.419][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:55.421][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:55.802][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2023-04-12 04:58:55.896][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:55.898][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:55.899][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:55.900][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:55.902][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:55.903][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:55.905][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:55.906][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:55.907][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:55.909][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:55.910][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:55.912][ef$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:55.914][biodb::testThat]
biodb.INFO [2023-04-12 04:58:55.915][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-04-12 04:58:55.917][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:55.918][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:55.921][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-04-12 04:58:55.981][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-12 04:58:55.983][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:55.985][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-12 04:58:56.008][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-04-12 04:58:56.011][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:58:56.012][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:58:56.014][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:56.016][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:56.037][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:56.039][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-12 04:58:56.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:56.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.053][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.TRACE[2023-04-12 04:58:56.055][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:56.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:56.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.059][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:56.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:56.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:56.104][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-04-12 04:58:56.105][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-04-12 04:58:56.123][biodb::testThat]
biodb.INFO [2023-04-12 04:58:56.124][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-04-12 04:58:56.125][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:56.126][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:56.133][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2023-04-12 04:58:56.135][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2023-04-12 04:58:56.136][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-12 04:58:56.137][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:56.139][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-12 04:58:56.141][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2023-04-12 04:58:56.142][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:58:56.143][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:58:56.144][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:56.145][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:56.164][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:56.165][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-12 04:58:56.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:56.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:56.179][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:56.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:56.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.183][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:56.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:56.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:56.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:56.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:56.217][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-04-12 04:58:56.218][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-04-12 04:58:56.219][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2023-04-12 04:58:56.231][biodb::testThat]
biodb.INFO [2023-04-12 04:58:56.232][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-04-12 04:58:56.233][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:56.234][biodb::testThat]
biodb.INFO [2023-04-12 04:58:56.254][biodb::testThat]
biodb.INFO [2023-04-12 04:58:56.255][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-04-12 04:58:56.256][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:56.257][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:56.260][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:56.261][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:56.263][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-12 04:58:56.264][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:56.265][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-12 04:58:56.270][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-12 04:58:56.271][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-12 04:58:56.272][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-12 04:58:56.273][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2023-04-12 04:58:56.279][biodb::testThat]
biodb.INFO [2023-04-12 04:58:56.280][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-04-12 04:58:56.281][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:56.282][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:56.285][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:56.286][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:56.288][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-12 04:58:56.289][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:56.296][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-12 04:58:56.301][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-12 04:58:56.302][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-12 04:58:56.303][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-12 04:58:56.304][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2023-04-12 04:58:56.318][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:56.319][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:56.321][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.322][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.323][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:56.324][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:56.325][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.326][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.327][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:56.328][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:56.329][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.330][ef$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:56.331][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-12 04:58:56.332][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-04-12 04:58:56.341][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-04-12 04:58:56.342][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-12 04:58:56.343][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.345][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.346][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.347][FUN] Functions in observer BiodbConfig: [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 [2023-04-12 04:58:56.352][biodb::testContext]
biodb.INFO [2023-04-12 04:58:56.353][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:58:56.354][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2023-04-12 04:58:56.355][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:58:56.356][biodb::testContext]
biodb.INFO [2023-04-12 04:58:56.363][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:58:56.365][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-12 04:58:56.369][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:56.370][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-12 04:58:56.371][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-12 04:58:56.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.375][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-12 04:58:56.376][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-12 04:58:56.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.380][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-12 04:58:56.381][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-12 04:58:56.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.384][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-12 04:58:56.385][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-12 04:58:56.386][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-12 04:58:56.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.389][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[2023-04-12 04:58:56.390][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-12 04:58:56.391][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-12 04:58:56.392][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-12 04:58:56.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.396][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-12 04:58:56.397][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-12 04:58:56.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.408][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-12 04:58:56.409][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-12 04:58:56.410][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-12 04:58:56.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.414][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-12 04:58:56.415][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-12 04:58:56.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.418][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-12 04:58:56.420][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-12 04:58:56.421][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-12 04:58:56.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.425][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:58:56.426][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-12 04:58:56.427][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-12 04:58:56.428][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-12 04:58:56.429][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-12 04:58:56.430][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-12 04:58:56.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.434][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-12 04:58:56.435][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-12 04:58:56.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.439][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-12 04:58:56.440][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-12 04:58:56.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.444][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-12 04:58:56.445][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-12 04:58:56.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.449][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-12 04:58:56.450][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-12 04:58:56.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.454][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-12 04:58:56.455][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-12 04:58:56.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.458][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:58:56.459][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-12 04:58:56.463][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-12 04:58:56.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.467][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-12 04:58:56.468][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-12 04:58:56.469][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-12 04:58:56.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.473][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-12 04:58:56.475][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:56.476][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-12 04:58:56.477][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.478][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:56.479][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.480][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:56.481][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:56.482][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:56.483][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:58:56.484][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:56.485][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.486][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-12 04:58:56.487][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:56.488][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.489][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.490][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:56.490][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:58:56.490][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:58:56.490][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:58:56.490][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:58:56.491][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:56.492][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:56.492][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:56.493][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:56.494][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:56.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:56.496][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:56.497][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.498][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:56.505][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:56.507][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:56.508][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.510][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-12 04:58:56.511][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:56.513][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:58:56.514][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.515][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:56.516][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.517][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:56.517][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:56.518][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:56.519][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:58:56.520][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:56.521][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.522][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-12 04:58:56.524][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:56.525][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.526][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.527][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:56.527][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:58:56.527][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:58:56.527][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:58:56.527][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:58:56.528][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:56.529][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:56.530][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:56.531][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:56.532][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:56.533][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:56.533][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:56.534][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.535][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:56.536][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:56.537][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:56.538][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.539][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-12 04:58:56.541][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.542][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-12 04:58:56.543][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.544][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:56.545][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.546][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:56.547][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:56.548][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:56.549][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:58:56.550][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:56.551][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:56.552][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-12 04:58:56.553][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:56.554][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.555][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.556][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.557][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:56.558][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:56.559][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:56.560][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:56.561][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:56.562][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:56.563][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:56.564][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.565][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:56.566][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:56.567][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:56.568][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.569][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-12 04:58:56.571][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.572][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:58:56.573][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.574][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:56.575][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.576][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:56.577][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:56.578][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:56.579][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:58:56.580][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:56.581][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:56.582][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-12 04:58:56.583][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:56.584][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.585][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:56.586][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.587][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:56.588][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:56.588][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:56.589][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:56.590][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:56.591][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:56.592][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:56.593][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.594][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:56.595][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:56.602][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:56.604][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:56.606][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:56.606][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.690][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-12 04:58:56.692][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-12 04:58:56.694][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-12 04:58:56.696][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-12 04:58:56.697][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 04:58:56.699][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-12 04:58:56.709][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-12 04:58:56.711][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-12 04:58:56.713][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-12 04:58:56.714][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-12 04:58:56.716][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:58:56.717][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-12 04:58:56.719][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-12 04:58:56.720][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-12 04:58:56.722][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-12 04:58:56.724][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 04:58:56.725][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-12 04:58:56.727][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-12 04:58:56.728][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 04:58:56.730][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-12 04:58:56.731][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-12 04:58:56.733][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-12 04:58:56.734][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-12 04:58:56.736][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-12 04:58:56.737][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-12 04:58:56.739][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-12 04:58:56.742][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-12 04:58:56.744][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-12 04:58:56.747][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-12 04:58:56.749][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-12 04:58:56.752][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-12 04:58:56.754][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-12 04:58:56.756][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-12 04:58:56.759][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-12 04:58:56.761][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-12 04:58:56.764][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-12 04:58:56.766][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-12 04:58:56.769][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-12 04:58:56.771][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-12 04:58:56.774][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-12 04:58:56.776][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-12 04:58:56.778][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-12 04:58:56.781][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-12 04:58:56.783][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-12 04:58:56.786][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-12 04:58:56.789][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-12 04:58:56.791][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-12 04:58:56.794][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-12 04:58:56.797][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-12 04:58:56.799][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-12 04:58:56.802][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-12 04:58:56.805][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-12 04:58:56.808][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-12 04:58:56.810][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-12 04:58:56.813][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-12 04:58:56.816][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-12 04:58:56.818][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-12 04:58:56.821][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-12 04:58:56.823][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-12 04:58:56.825][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-12 04:58:56.827][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-12 04:58:56.830][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-12 04:58:56.832][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-12 04:58:56.834][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-12 04:58:56.837][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-12 04:58:56.839][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-12 04:58:56.842][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 04:58:56.856][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 04:58:56.859][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-12 04:58:56.861][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-12 04:58:56.863][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-12 04:58:56.864][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-12 04:58:56.866][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-12 04:58:56.867][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-12 04:58:56.869][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-12 04:58:56.870][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-12 04:58:56.872][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-12 04:58:56.873][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-12 04:58:56.875][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-12 04:58:56.876][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-12 04:58:56.878][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-12 04:58:56.879][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-12 04:58:56.881][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-12 04:58:56.882][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-12 04:58:56.884][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:58:56.886][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:56.887][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.890][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:56.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:56.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:56.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:56.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:56.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:56.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:56.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:57.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:57.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:57.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:57.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:57.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:57.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:57.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:57.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:57.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:57.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:57.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:57.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:57.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:57.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:57.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:57.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:57.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:57.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:57.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:57.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:57.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:57.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:57.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:57.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:57.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:57.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.057][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-04-12 04:58:57.058][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-04-12 04:58:57.061][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:57.062][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-12 04:58:57.063][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.064][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:57.065][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:57.066][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-04-12 04:58:57.067][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.068][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:57.069][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-12 04:58:57.070][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:57.071][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.072][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-04-12 04:58:57.073][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-04-12 04:58:57.075][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:57.076][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:57.076][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-04-12 04:58:57.076][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2023-04-12 04:58:57.077][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-12 04:58:57.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:57.078][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:57.079][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:57.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:57.081][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:57.082][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:57.083][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-12 04:58:57.083][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-04-12 04:58:57.084][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:57.085][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:57.085][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.086][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:57.088][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2023-04-12 04:58:57.089][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-12 04:58:57.091][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-12 04:58:57.092][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:58:57.094][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 04:58:57.103][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-04-12 04:58:57.105][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-04-12 04:58:57.106][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-12 04:58:57.108][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-12 04:58:57.109][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:57.110][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:57.112][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-04-12 04:58:57.113][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-04-12 04:58:57.114][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-12 04:58:57.114][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-04-12 04:58:57.115][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:57.116][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:57.117][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-04-12 04:58:57.117][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-04-12 04:58:57.119][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-12 04:58:57.120][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-12 04:58:57.121][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:57.122][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:57.124][private$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[2023-04-12 04:58:57.125][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:57.126][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-04-12 04:58:57.128][biodb::testThat]
biodb.INFO [2023-04-12 04:58:57.129][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2023-04-12 04:58:57.130][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:57.131][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:57.135][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:57.137][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:57.138][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-12 04:58:57.140][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:57.141][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-12 04:58:57.145][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-12 04:58:57.146][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-12 04:58:57.147][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-12 04:58:57.148][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-12 04:58:57.151][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2023-04-12 04:58:57.153][biodb::testThat]
biodb.INFO [2023-04-12 04:58:57.154][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2023-04-12 04:58:57.155][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:57.156][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:57.159][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-04-12 04:58:57.160][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-12 04:58:57.162][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:57.163][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-12 04:58:57.165][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-04-12 04:58:57.166][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:57.168][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-04-12 04:58:57.170][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:57.187][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:57.188][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-12 04:58:57.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:57.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:57.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:57.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:57.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:57.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.208][FUN] Functions in observer BiodbConfig: [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[2023-04-12 04:58:57.213][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.214][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.216][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.217][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.225][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:57.226][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:57.227][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.228][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.230][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:57.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:57.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.237][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:57.238][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:57.239][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.240][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.241][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:57.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:57.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.248][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:57.250][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:57.251][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.252][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.253][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:57.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:57.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.260][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.261][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.262][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.263][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.271][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:57.272][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:57.273][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.274][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:57.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:57.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.282][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:57.284][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:57.285][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.286][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.287][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:57.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:57.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.294][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:57.295][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:57.296][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.297][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.298][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:57.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:57.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.306][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:57.312][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:57.313][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.314][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.316][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:57.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:57.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.323][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:57.324][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:57.325][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.326][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.327][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:57.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:57.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.334][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:57.335][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:57.336][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.337][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.339][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:57.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:57.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.346][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:57.347][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:57.348][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.349][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.351][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:57.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:57.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.358][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.359][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.360][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.361][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.363][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.370][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.371][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.372][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.373][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.381][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:57.382][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:57.383][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.384][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:57.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:57.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.392][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:57.393][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:57.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.395][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.396][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:57.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:57.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.403][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:57.404][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:57.405][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.406][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.408][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:57.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:57.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.420][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-12 04:58:57.422][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:57.422][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.423][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.425][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-12 04:58:57.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:57.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.444][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:57.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:57.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.448][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:57.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:57.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.452][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:57.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:57.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.456][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:57.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:57.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.460][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:57.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:57.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.464][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:57.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:57.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:57.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:57.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:57.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:57.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:57.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:57.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:57.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.490][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:57.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:57.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.494][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:57.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:57.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:57.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:57.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.507][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:57.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:57.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.512][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:57.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:57.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.516][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:57.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:57.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.520][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:57.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:57.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.524][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:57.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:57.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.528][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:57.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:57.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.532][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:57.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:57.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.535][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:57.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:57.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.539][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:57.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:57.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.543][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:57.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:57.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.547][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:57.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:57.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.551][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:57.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:57.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:57.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:57.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:57.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:57.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:57.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:57.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.579][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:57.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:57.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.584][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:57.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:57.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.587][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:57.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:57.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:57.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.610][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:57.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:57.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:57.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:57.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.619][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:57.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:57.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.624][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:57.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:57.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.628][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:57.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:57.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.632][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:57.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:57.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.636][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:57.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:57.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.639][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:57.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:57.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.643][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:57.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:57.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.647][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:57.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:57.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.651][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:57.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:57.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.655][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:57.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:57.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.659][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-12 04:58:57.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.675][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-12 04:58:57.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:57.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:57.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:57.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:57.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:57.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:57.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:57.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:57.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:57.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:57.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:57.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.713][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:57.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:57.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.717][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:57.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:57.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.724][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:57.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:57.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:57.756][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-04-12 04:58:57.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:57.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:57.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:57.772][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-12 04:58:57.773][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-04-12 04:58:57.774][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-04-12 04:58:57.775][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-12 04:58:57.776][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:57.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:57.778][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:57.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:57.780][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-12 04:58:57.784][biodb::testContext]
biodb.INFO [2023-04-12 04:58:57.785][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:58:57.786][biodb::testContext] Test context - Test search of entries
biodb.INFO [2023-04-12 04:58:57.787][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:58:57.788][biodb::testContext]
biodb.INFO [2023-04-12 04:58:57.818][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:58:57.820][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-12 04:58:57.824][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:57.825][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-12 04:58:57.826][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-12 04:58:57.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.830][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-12 04:58:57.831][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-12 04:58:57.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.834][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-12 04:58:57.835][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-12 04:58:57.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.839][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-12 04:58:57.840][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-12 04:58:57.841][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-12 04:58:57.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.844][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-12 04:58:57.845][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-12 04:58:57.846][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-12 04:58:57.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.850][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-12 04:58:57.851][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-12 04:58:57.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.855][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-12 04:58:57.856][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-12 04:58:57.857][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-12 04:58:57.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.860][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-12 04:58:57.861][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-12 04:58:57.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.865][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-12 04:58:57.866][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-12 04:58:57.867][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-12 04:58:57.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.871][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:58:57.872][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-12 04:58:57.873][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-12 04:58:57.874][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-12 04:58:57.875][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-12 04:58:57.876][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-12 04:58:57.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.880][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-12 04:58:57.881][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-12 04:58:57.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.885][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-12 04:58:57.886][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-12 04:58:57.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.889][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-12 04:58:57.890][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-12 04:58:57.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.894][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-12 04:58:57.895][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-12 04:58:57.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.899][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-12 04:58:57.900][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-12 04:58:57.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.904][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:58:57.905][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-12 04:58:57.910][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-12 04:58:57.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.922][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-12 04:58:57.924][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-12 04:58:57.926][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-12 04:58:57.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:57.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:57.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:57.931][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-12 04:58:57.933][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:57.934][self$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[2023-04-12 04:58:57.935][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.936][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:57.937][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.938][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:57.939][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:57.940][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:57.942][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:58:57.943][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:57.944][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.945][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-12 04:58:57.946][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:57.947][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:57.948][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.949][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:57.949][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:58:57.949][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:58:57.949][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:58:57.949][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:58:57.950][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:57.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:57.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:57.954][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:57.955][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:57.956][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:57.957][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:57.958][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:57.959][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:57.960][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:57.961][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:57.962][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:57.963][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-12 04:58:57.966][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:57.967][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:58:57.968][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.969][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:57.970][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.971][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:57.972][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:57.973][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:57.974][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:58:57.975][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:57.976][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.977][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-12 04:58:57.978][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:57.979][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:57.980][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.981][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:57.981][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:58:57.981][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:58:57.981][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:58:57.981][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:58:57.982][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:57.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:57.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:57.985][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:57.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:57.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:57.988][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:57.989][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:57.990][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:57.991][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:57.992][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:57.993][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:57.994][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-12 04:58:57.996][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.997][self$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[2023-04-12 04:58:57.998][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:57.999][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:58.000][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:58.001][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:58.002][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:58.003][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:58.004][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:58:58.005][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:58.006][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:58.007][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-12 04:58:58.008][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:58.009][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:58.010][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:58.011][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:58.013][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:58.014][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:58.014][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:58.015][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:58.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:58.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:58.018][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:58.026][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:58.027][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:58.028][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:58.030][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:58.031][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:58.033][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-12 04:58:58.034][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:58.035][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:58:58.036][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:58.037][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:58.038][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:58.039][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:58.040][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:58.041][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:58.042][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:58:58.043][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:58.044][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:58.046][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-12 04:58:58.047][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:58.048][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:58.049][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:58.050][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:58.051][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:58.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:58.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:58.054][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:58.055][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:58.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:58.057][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:58.058][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:58.059][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:58.060][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:58.061][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:58.062][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:58.063][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:58.064][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.070][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[2023-04-12 04:58:58.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.079][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[2023-04-12 04:58:58.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.088][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[2023-04-12 04:58:58.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.092][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[2023-04-12 04:58:58.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.105][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[2023-04-12 04:58:58.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.110][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[2023-04-12 04:58:58.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.135][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[2023-04-12 04:58:58.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.139][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[2023-04-12 04:58:58.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.143][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[2023-04-12 04:58:58.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.148][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[2023-04-12 04:58:58.149][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-12 04:58:58.150][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-12 04:58:58.151][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-12 04:58:58.153][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-12 04:58:58.154][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 04:58:58.155][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-12 04:58:58.157][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-12 04:58:58.158][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-12 04:58:58.159][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-12 04:58:58.161][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-12 04:58:58.162][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:58:58.163][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-12 04:58:58.165][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-12 04:58:58.166][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-12 04:58:58.167][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-12 04:58:58.169][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 04:58:58.170][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-12 04:58:58.171][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-12 04:58:58.173][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 04:58:58.174][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-12 04:58:58.175][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-12 04:58:58.177][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-12 04:58:58.178][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-12 04:58:58.179][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-12 04:58:58.181][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-12 04:58:58.182][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-12 04:58:58.183][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-12 04:58:58.185][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-12 04:58:58.186][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-12 04:58:58.187][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-12 04:58:58.189][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-12 04:58:58.190][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-12 04:58:58.191][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-12 04:58:58.193][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-12 04:58:58.194][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-12 04:58:58.195][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-12 04:58:58.197][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-12 04:58:58.198][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-12 04:58:58.199][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-12 04:58:58.200][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-12 04:58:58.202][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-12 04:58:58.203][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-12 04:58:58.204][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-12 04:58:58.206][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-12 04:58:58.207][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-12 04:58:58.208][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-12 04:58:58.215][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-12 04:58:58.217][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-12 04:58:58.219][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-12 04:58:58.221][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-12 04:58:58.222][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-12 04:58:58.223][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-12 04:58:58.225][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-12 04:58:58.226][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-12 04:58:58.228][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-12 04:58:58.229][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-12 04:58:58.230][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-12 04:58:58.231][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-12 04:58:58.233][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-12 04:58:58.234][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-12 04:58:58.235][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-12 04:58:58.237][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-12 04:58:58.238][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-12 04:58:58.239][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-12 04:58:58.241][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-12 04:58:58.242][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-12 04:58:58.243][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 04:58:58.245][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 04:58:58.246][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-12 04:58:58.247][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-12 04:58:58.249][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-12 04:58:58.250][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-12 04:58:58.251][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-12 04:58:58.253][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-12 04:58:58.254][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-12 04:58:58.255][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-12 04:58:58.257][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-12 04:58:58.258][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-12 04:58:58.259][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-12 04:58:58.261][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-12 04:58:58.262][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-12 04:58:58.263][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-12 04:58:58.265][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-12 04:58:58.266][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-12 04:58:58.268][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:58:58.269][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:58.269][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.271][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.272][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[2023-04-12 04:58:58.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.289][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[2023-04-12 04:58:58.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.334][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.DEBUG[2023-04-12 04:58:58.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.359][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[2023-04-12 04:58:58.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.372][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[2023-04-12 04:58:58.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:58.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:58.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.384][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[2023-04-12 04:58:58.385][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2023-04-12 04:58:58.387][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2023-04-12 04:58:58.389][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:58.390][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-12 04:58:58.391][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:58.392][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:58.393][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:58.394][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2023-04-12 04:58:58.400][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:58.401][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:58.402][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-04-12 04:58:58.404][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:58.405][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:58.406][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2023-04-12 04:58:58.407][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2023-04-12 04:58:58.408][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2023-04-12 04:58:58.409][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:58.410][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:58.410][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2023-04-12 04:58:58.410][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2023-04-12 04:58:58.411][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-12 04:58:58.412][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:58.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:58.414][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:58.414][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:58.415][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:58.416][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:58.417][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-12 04:58:58.417][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2023-04-12 04:58:58.418][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:58.419][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:58.420][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:58.421][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:58.423][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2023-04-12 04:58:58.424][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-12 04:58:58.426][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-12 04:58:58.427][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:58:58.429][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 04:58:58.432][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2023-04-12 04:58:58.433][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2023-04-12 04:58:58.435][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-12 04:58:58.436][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-12 04:58:58.438][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:58.439][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:58.440][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2023-04-12 04:58:58.441][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2023-04-12 04:58:58.442][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2023-04-12 04:58:58.442][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2023-04-12 04:58:58.444][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:58.445][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:58.445][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2023-04-12 04:58:58.446][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2023-04-12 04:58:58.448][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2023-04-12 04:58:58.449][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-12 04:58:58.450][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:58.451][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:58.453][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2023-04-12 04:58:58.454][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-12 04:58:58.455][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2023-04-12 04:58:58.457][biodb::testThat]
biodb.INFO [2023-04-12 04:58:58.458][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2023-04-12 04:58:58.458][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:58.459][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:58.471][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-04-12 04:58:58.472][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2023-04-12 04:58:58.473][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2023-04-12 04:58:58.476][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:58.478][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:58.479][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-12 04:58:58.480][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:58.481][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-12 04:58:58.485][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-12 04:58:58.486][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-12 04:58:58.487][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-12 04:58:58.488][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-12 04:58:58.489][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-12 04:58:58.490][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2023-04-12 04:58:58.492][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2023-04-12 04:58:58.493][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-12 04:58:58.495][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:58.503][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-12 04:58:58.505][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2023-04-12 04:58:58.507][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:58.509][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2023-04-12 04:58:58.510][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:58.527][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:58.529][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-12 04:58:58.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:58.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:58.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:58.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:58.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:58.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:58.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:58.545][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.546][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.547][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.548][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.556][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:58.558][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:58.558][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.559][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.561][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:58.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:58.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.568][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:58.569][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:58.570][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.571][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.573][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:58.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:58.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.579][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:58.580][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:58.581][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.582][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.583][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:58.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:58.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.590][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.591][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.592][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.593][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.606][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:58.608][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:58.609][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.610][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:58.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:58.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.629][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:58.630][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:58.631][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.632][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.634][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:58.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:58.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.642][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:58.644][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:58.645][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.646][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.648][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:58.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:58.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.655][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:58.657][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:58.658][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.659][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.660][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:58.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:58.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.668][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:58.670][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:58.671][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.672][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.673][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:58.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:58.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.681][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:58.682][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:58.683][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.684][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.685][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:58.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:58.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.693][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:58.694][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:58.695][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.696][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:58.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:58.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.705][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.706][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.707][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.708][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.718][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.719][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.720][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.721][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.745][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:58.746][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:58.747][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.748][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.749][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:58.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:58.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.756][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:58.757][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:58.758][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.759][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.760][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:58.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:58.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.767][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:58.768][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:58.769][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.770][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.772][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:58.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:58.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.779][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-12 04:58:58.781][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:58.782][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.783][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.784][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-12 04:58:58.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:58.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:58.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:58.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.803][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:58.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:58.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.807][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:58.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:58.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.811][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:58.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:58.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.815][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:58.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:58.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.819][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:58.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:58.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.823][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:58.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:58.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:58.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:58.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:58.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:58.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:58.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:58.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:58.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.859][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:58.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:58.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.864][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:58.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:58.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.868][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:58.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:58.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.872][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:58.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:58.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:58.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:58.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.881][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:58.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:58.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.885][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:58.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:58.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.889][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:58.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:58.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.893][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:58.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:58.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.897][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:58.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:58.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.901][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:58.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:58.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.905][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:58.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:58.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.910][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:58.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:58.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.914][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:58.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:58.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.918][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:58.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:58.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:58.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:58.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:58.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:58.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.931][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:58.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:58.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.941][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.945][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:58.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.953][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:58.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:58.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.956][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:58.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:58.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.960][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:58.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:58.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:58.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:58.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.979][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:58.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:58.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:58.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:58.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.987][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:58.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:58.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.991][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:58.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:58.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.995][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:58.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:58.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.999][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.003][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.007][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.010][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:59.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:59.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.014][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:59.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:59.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.018][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:59.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:59.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.022][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-12 04:58:59.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.032][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.044][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-12 04:58:59.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.055][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.058][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.062][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.073][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:59.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:59.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.077][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:59.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:59.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.084][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:59.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:59.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:59.112][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2023-04-12 04:58:59.113][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.123][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.127][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.131][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:59.135][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-12 04:58:59.135][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-12 04:58:59.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:59.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:59.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:59.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:59.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:59.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:59.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:59.147][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2023-04-12 04:58:59.148][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2023-04-12 04:58:59.150][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:59.151][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2023-04-12 04:58:59.153][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2023-04-12 04:58:59.155][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:59.156][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2023-04-12 04:58:59.157][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:59.175][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:59.177][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2023-04-12 04:58:59.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:59.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:59.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:59.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:59.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:59.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:59.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:59.191][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.192][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.193][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.194][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.201][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.202][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.203][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.204][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.205][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.217][ef$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:59.218][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:59.219][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.220][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.222][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:59.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:59.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.229][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:59.230][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:59.230][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.231][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.233][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:59.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:59.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.239][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.240][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.241][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.242][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.250][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:59.251][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:59.252][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.253][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:59.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:59.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.261][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:59.262][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:59.263][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.263][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.265][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:59.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:59.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.271][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:59.272][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:59.273][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.274][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.275][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:59.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:59.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.282][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:59.283][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:59.284][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.285][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.286][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:59.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:59.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.292][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:59.293][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:59.294][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.295][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.297][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:59.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:59.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.303][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:59.304][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:59.305][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.306][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:59.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:59.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.320][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:59.321][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:59.322][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.323][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:59.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:59.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.330][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.331][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.332][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.333][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.341][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.342][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.343][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.344][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.351][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.352][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.353][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.354][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.355][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.362][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.363][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.364][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.365][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.366][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.372][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:59.373][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:59.374][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.375][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.376][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:59.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:59.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.383][ef$get] Asked field names are: super.class.
biodb.TRACE[2023-04-12 04:58:59.384][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:59.385][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.385][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.387][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2023-04-12 04:58:59.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:59.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.411][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:59.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:59.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.415][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:59.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:59.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.418][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:59.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:59.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.422][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:59.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:59.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.426][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:59.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:59.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.430][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-12 04:58:59.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-12 04:58:59.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:59.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:59.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:59.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:59.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:59.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:59.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2023-04-12 04:58:59.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.456][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:59.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:59.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.460][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:59.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:59.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.464][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:59.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:59.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.467][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:59.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:59.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.471][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:59.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:59.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.475][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:59.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2023-04-12 04:58:59.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.479][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:59.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:59.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.482][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:59.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:59.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.486][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:59.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2023-04-12 04:58:59.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.494][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.499][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.503][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.507][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:59.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:59.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.511][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:59.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:59.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.515][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:59.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:59.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:59.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:59.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:59.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:59.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.526][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-12 04:58:59.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-12 04:58:59.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.530][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.534][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.542][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:59.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:59.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.545][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:59.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:59.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.549][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:59.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:59.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:59.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.572][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.575][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:59.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:59.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.584][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:59.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:59.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.588][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:59.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:59.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.592][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.596][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.600][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2023-04-12 04:58:59.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.603][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:59.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:59.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.607][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:59.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:59.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.611][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-04-12 04:58:59.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-04-12 04:58:59.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.615][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-12 04:58:59.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.619][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.630][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2023-04-12 04:58:59.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-12 04:58:59.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.649][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:59.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:59.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.660][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:59.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:59.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.664][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:59.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:59.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.677][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:59.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:59.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:59.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:59.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:59.708][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2023-04-12 04:58:59.709][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.713][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.716][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.720][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:59.724][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-12 04:58:59.725][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2023-04-12 04:58:59.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:59.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:59.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:59.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:59.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:59.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:59.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:59.747][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-04-12 04:58:59.748][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-04-12 04:58:59.749][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2023-04-12 04:58:59.750][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:59.752][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:59.753][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-12 04:58:59.754][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:58:59.755][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-12 04:58:59.759][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-12 04:58:59.760][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-12 04:58:59.761][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-12 04:58:59.762][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-12 04:58:59.763][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-12 04:58:59.769][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-12 04:58:59.771][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.776][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.779][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.783][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.787][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.791][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.794][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:59.798][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-12 04:58:59.799][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-12 04:58:59.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:59.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:59.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:59.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:59.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:59.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:59.810][FUN] Functions in observer BiodbConfig: [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[2023-04-12 04:58:59.811][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.815][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.818][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.822][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.826][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.830][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:59.833][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:58:59.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:58:59.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:59.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:59.837][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-04-12 04:58:59.838][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-12 04:58:59.839][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:59.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:59.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:59.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:59.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:59.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:59.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:00.038][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2023-04-12 04:59:00.039][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-04-12 04:59:00.040][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2023-04-12 04:59:00.042][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:59:00.043][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:59:00.045][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2023-04-12 04:59:00.046][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2023-04-12 04:59:00.047][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2023-04-12 04:59:00.051][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2023-04-12 04:59:00.052][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2023-04-12 04:59:00.053][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2023-04-12 04:59:00.054][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2023-04-12 04:59:00.055][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2023-04-12 04:59:00.055][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2023-04-12 04:59:00.057][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.061][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.065][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.068][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.072][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.076][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.079][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:00.083][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2023-04-12 04:59:00.084][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2023-04-12 04:59:00.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:00.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:00.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:00.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:00.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:00.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:00.094][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.TRACE[2023-04-12 04:59:00.095][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.099][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.103][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.106][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.110][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.114][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:00.118][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-12 04:59:00.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-12 04:59:00.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:00.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:00.121][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2023-04-12 04:59:00.122][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2023-04-12 04:59:00.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:00.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:00.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:00.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:00.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:00.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:00.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-12 04:59:00.137][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-12 04:59:00.138][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2023-04-12 04:59:00.139][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2023-04-12 04:59:00.140][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-12 04:59:00.141][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:00.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:00.142][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:00.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:00.144][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:00.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 199 ]
>
> proc.time()
user system elapsed
10.041 0.306 11.721
biodbHmdb.Rcheck/biodbHmdb-Ex.timings
| name | user | system | elapsed | |
| HmdbMetabolitesConn | 0.498 | 0.025 | 0.524 | |
| HmdbMetabolitesEntry | 0.115 | 0.016 | 0.131 | |