Back to Mac ARM64 build report for BioC 3.17
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 199/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.6.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_17
git_last_commit: 3555696
git_last_commit_date: 2023-04-25 11:34:40 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for biodbLipidmaps on kjohnson2


To the developers/maintainers of the biodbLipidmaps package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: biodbLipidmaps
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.6.0.tar.gz
StartedAt: 2023-10-17 05:44:14 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 05:47:20 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 186.2 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/biodbLipidmaps.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
LipidmapsStructureConn 2.614  0.728   5.647
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2023-10-17 05:45:13.864][biodb::testContext]
biodb.INFO [2023-10-17 05:45:13.870][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:45:13.872][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-10-17 05:45:13.875][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:45:13.877][biodb::testContext]
biodb.INFO [2023-10-17 05:45:13.887][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:45:13.895][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-17 05:45:13.910][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:45:13.913][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-17 05:45:13.915][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-17 05:45:13.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:13.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:13.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:13.924][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-17 05:45:13.962][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-17 05:45:13.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:13.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:13.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:13.970][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-17 05:45:13.974][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-17 05:45:13.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:13.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:13.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:13.982][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-17 05:45:13.985][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-17 05:45:13.987][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-17 05:45:13.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:13.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:13.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:13.997][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-17 05:45:13.999][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-17 05:45:14.004][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-17 05:45:14.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.013][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-17 05:45:14.015][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-17 05:45:14.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.024][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-17 05:45:14.026][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-17 05:45:14.028][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-17 05:45:14.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.036][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-17 05:45:14.037][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-17 05:45:14.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.043][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-17 05:45:14.048][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-17 05:45:14.049][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-17 05:45:14.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.059][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:45:14.063][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-17 05:45:14.064][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-17 05:45:14.067][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-17 05:45:14.069][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-17 05:45:14.070][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-17 05:45:14.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.080][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-17 05:45:14.081][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-17 05:45:14.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.089][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-17 05:45:14.092][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-17 05:45:14.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.100][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-17 05:45:14.105][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-17 05:45:14.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.112][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-17 05:45:14.114][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-17 05:45:14.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.120][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-17 05:45:14.122][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-17 05:45:14.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.129][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:45:14.132][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-17 05:45:14.166][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-17 05:45:14.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.171][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-17 05:45:14.172][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-17 05:45:14.174][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-17 05:45:14.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.187][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-17 05:45:14.261][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.285][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-17 05:45:14.286][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.288][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:45:14.289][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.290][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.295][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.296][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.298][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:45:14.299][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:45:14.300][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.301][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-17 05:45:14.303][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:45:14.304][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.305][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.307][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:45:14.307][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:45:14.307][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:45:14.307][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:45:14.307][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:45:14.308][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:45:14.309][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:14.310][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:14.311][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:45:14.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:14.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:14.317][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.319][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.321][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:45:14.322][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:45:14.323][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.325][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.326][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-17 05:45:14.328][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.330][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:45:14.331][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.335][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:45:14.337][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.338][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.340][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.342][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.343][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:45:14.345][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:45:14.346][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.348][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-17 05:45:14.349][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:45:14.350][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.352][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.356][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:45:14.356][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:45:14.356][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:45:14.356][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:45:14.356][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:45:14.358][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:45:14.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:14.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:14.362][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:45:14.363][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:14.366][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:14.367][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.368][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.372][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:45:14.373][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:45:14.375][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.376][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.378][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-17 05:45:14.380][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.382][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-17 05:45:14.383][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.384][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:45:14.386][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.387][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.389][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.393][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.395][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:45:14.397][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:45:14.399][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.400][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-17 05:45:14.401][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:45:14.403][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.405][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.407][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.409][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:45:14.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:14.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:14.414][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:45:14.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:14.419][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:14.420][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.422][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.423][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:45:14.424][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:45:14.427][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.428][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.429][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-17 05:45:14.432][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.435][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:45:14.436][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.438][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:45:14.439][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.440][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.443][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.445][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.447][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:45:14.450][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:45:14.451][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.452][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-17 05:45:14.455][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:45:14.456][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.458][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.460][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.462][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:45:14.465][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:14.466][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:14.468][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:45:14.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:14.471][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:14.473][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.475][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.476][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:45:14.477][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:45:14.482][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.484][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:14.493][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:45:14.494][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.604][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-17 05:45:14.611][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-17 05:45:14.613][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-17 05:45:14.615][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-17 05:45:14.617][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-17 05:45:14.618][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-17 05:45:14.620][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-17 05:45:14.622][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-17 05:45:14.627][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-17 05:45:14.630][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-17 05:45:14.632][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-17 05:45:14.634][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-17 05:45:14.636][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-17 05:45:14.638][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-17 05:45:14.651][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-17 05:45:14.652][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-17 05:45:14.654][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-17 05:45:14.656][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-17 05:45:14.658][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-17 05:45:14.660][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-17 05:45:14.662][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-17 05:45:14.664][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-17 05:45:14.666][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-17 05:45:14.668][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-17 05:45:14.670][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-17 05:45:14.673][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-17 05:45:14.675][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-17 05:45:14.677][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-17 05:45:14.678][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-17 05:45:14.680][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-17 05:45:14.682][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-17 05:45:14.684][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-17 05:45:14.686][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-17 05:45:14.688][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-17 05:45:14.689][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-17 05:45:14.691][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-17 05:45:14.694][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-17 05:45:14.696][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-17 05:45:14.697][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-17 05:45:14.699][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-17 05:45:14.701][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-17 05:45:14.703][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-17 05:45:14.704][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-17 05:45:14.706][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-17 05:45:14.708][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-17 05:45:14.710][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-17 05:45:14.712][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-17 05:45:14.715][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-17 05:45:14.717][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-17 05:45:14.719][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-17 05:45:14.720][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-17 05:45:14.722][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-17 05:45:14.723][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-17 05:45:14.725][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-17 05:45:14.726][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-17 05:45:14.729][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-17 05:45:14.731][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-17 05:45:14.733][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-17 05:45:14.734][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-17 05:45:14.736][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-17 05:45:14.738][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-17 05:45:14.741][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-17 05:45:14.743][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-17 05:45:14.745][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-17 05:45:14.747][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-17 05:45:14.749][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-17 05:45:14.751][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-17 05:45:14.753][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-17 05:45:14.754][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-17 05:45:14.756][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-17 05:45:14.758][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-17 05:45:14.759][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-17 05:45:14.761][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-17 05:45:14.763][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-17 05:45:14.765][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-17 05:45:14.766][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-17 05:45:14.768][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-17 05:45:14.770][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-17 05:45:14.772][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-17 05:45:14.774][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-17 05:45:14.776][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-17 05:45:14.778][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-17 05:45:14.779][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-17 05:45:14.787][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-17 05:45:14.789][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:45:14.793][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:45:14.795][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.797][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.810][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.DEBUG[2023-10-17 05:45:14.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.879][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[2023-10-17 05:45:14.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:14.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:14.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:14.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:14.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:14.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:14.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:14.946][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-10-17 05:45:14.958][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-10-17 05:45:14.969][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.970][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.971][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.973][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:45:14.974][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.976][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.978][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.979][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:45:14.981][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:45:14.982][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:45:14.983][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:14.985][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-10-17 05:45:14.986][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:45:14.988][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-10-17 05:45:14.988][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-10-17 05:45:14.988][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-10-17 05:45:14.988][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-10-17 05:45:14.988][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-10-17 05:45:14.988][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-10-17 05:45:14.988][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-10-17 05:45:14.988][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-10-17 05:45:14.988][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-10-17 05:45:14.990][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:14.992][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:45:14.992][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:45:14.994][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:45:14.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:14.996][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:14.998][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:45:15.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:15.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:15.003][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:45:15.005][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-17 05:45:15.005][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-10-17 05:45:15.007][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:45:15.008][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:45:15.010][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:15.011][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:15.017][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-10-17 05:45:15.020][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-17 05:45:15.058][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-10-17 05:45:15.059][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-10-17 05:45:15.065][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-10-17 05:45:15.072][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-10-17 05:45:15.080][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-17 05:45:15.081][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-17 05:45:15.083][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-10-17 05:45:15.084][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-10-17 05:45:15.095][biodb::testThat]
biodb.INFO [2023-10-17 05:45:15.097][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-10-17 05:45:15.098][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:45:15.099][biodb::testThat]
biodb.TRACE[2023-10-17 05:45:15.105][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2023-10-17 05:45:15.107][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:45:15.112][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-17 05:45:15.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:45:15.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:15.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:15.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:15.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:15.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:15.147][FUN] Functions in observer BiodbConfig: [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[2023-10-17 05:45:15.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:45:15.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:45:15.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.194][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:45:15.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:45:15.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.199][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:45:15.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:45:15.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.205][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.244][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.251][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.256][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.261][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:45:15.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.266][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:45:15.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.271][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:15.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:15.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.276][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:15.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:15.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.292][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:45:15.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.297][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-17 05:45:15.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.307][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.318][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:45:15.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.407][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.425][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.431][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.443][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:45:15.478][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-10-17 05:45:15.481][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:45:15.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:45:15.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.487][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:45:15.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:45:15.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.493][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-17 05:45:15.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-17 05:45:15.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.500][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-17 05:45:15.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-17 05:45:15.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.551][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.607][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.612][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.618][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:15.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.651][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.652][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.653][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.654][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.678][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.683][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.684][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.686][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.687][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.689][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.705][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.710][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.715][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.720][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.722][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.723][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.724][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.726][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.740][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:15.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:15.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.748][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:15.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:15.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.754][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:15.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:15.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.764][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:15.765][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:15.766][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.768][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.769][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:15.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:15.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.802][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.803][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.805][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.806][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.823][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.828][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.833][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.838][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.839][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.840][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.842][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.843][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.857][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:15.859][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:15.861][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.862][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.871][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.872][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:15.873][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.875][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.885][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:15.888][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:15.889][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.890][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.901][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.947][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:15.950][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.952][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.963][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:15.964][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:15.965][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.969][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:15.978][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.982][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:15.983][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:15.986][ef$get] fields variable is a list.
biodb.INFO [2023-10-17 05:45:16.005][biodb::testThat]
biodb.INFO [2023-10-17 05:45:16.006][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-10-17 05:45:16.007][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:45:16.011][biodb::testThat]
biodb.DEBUG[2023-10-17 05:45:16.036][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-10-17 05:45:16.051][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:45:16.058][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-10-17 05:45:16.062][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:45:16.064][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-10-17 05:45:16.068][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:45:16.107][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:45:16.109][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-17 05:45:16.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:45:16.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:16.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:16.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:16.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:16.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:16.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:45:16.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:16.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:16.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:16.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:16.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:45:16.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:45:16.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:45:16.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:45:16.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.178][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:45:16.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:45:16.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.187][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:45:16.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:45:16.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.194][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:16.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:16.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.203][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:16.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:16.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.212][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:16.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:16.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.220][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:16.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:16.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.228][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:45:16.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:16.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.237][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:45:16.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:16.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.244][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:16.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:16.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.253][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:16.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:16.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.260][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:16.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:16.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.277][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:45:16.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.284][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-17 05:45:16.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:16.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:16.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.303][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:45:16.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:16.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.320][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:16.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.328][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:16.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.345][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:16.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:16.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.355][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:16.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:16.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.360][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:16.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:16.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:16.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:16.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.369][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:16.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:16.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:16.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:16.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:16.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:16.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:16.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:16.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:16.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:16.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:16.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:16.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:16.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:16.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:45:16.412][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-10-17 05:45:16.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-10-17 05:45:16.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-10-17 05:45:16.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-10-17 05:45:16.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-10-17 05:45:16.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-10-17 05:45:16.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-10-17 05:45:16.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-17 05:45:16.440][biodb::testThat]
biodb.INFO [2023-10-17 05:45:16.443][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-10-17 05:45:16.444][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:45:16.445][biodb::testThat]
biodb.TRACE[2023-10-17 05:45:16.449][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:16.450][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.451][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.453][ef$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:45:16.455][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-10-17 05:45:16.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:16.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:16.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:16.503][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:16.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:16.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:16.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:45:16.510][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-10-17 05:45:16.517][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-10-17 05:45:16.540][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:45:16.541][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:45:16.543][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-10-17 05:45:17.590][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-10-17 05:45:18.443][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:45:18.449][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-10-17 05:45:18.468][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-10-17 05:45:18.472][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-10-17 05:45:18.489][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:18.492][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:18.493][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:18.494][ef$get] fields variable is a list.
biodb.INFO [2023-10-17 05:45:18.504][biodb::testThat]
biodb.INFO [2023-10-17 05:45:18.506][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-10-17 05:45:18.508][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:45:18.509][biodb::testThat]
biodb.TRACE[2023-10-17 05:45:18.548][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:18.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:18.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:18.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:18.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:18.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:18.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:18.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:18.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:18.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:18.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:18.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:45:18.742][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-10-17 05:45:18.746][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:45:18.771][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-10-17 05:45:18.773][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:45:18.776][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-10-17 05:45:18.806][biodb::testThat]
biodb.INFO [2023-10-17 05:45:18.808][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-10-17 05:45:18.809][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:45:18.813][biodb::testThat]
biodb.TRACE[2023-10-17 05:45:18.856][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:45:18.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:45:18.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:18.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:18.864][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:45:18.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:45:18.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:18.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:18.871][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-17 05:45:18.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-17 05:45:18.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:18.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:18.880][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-17 05:45:18.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-17 05:45:18.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:18.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:18.941][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:45:18.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:45:18.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:18.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:18.950][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:45:18.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:45:18.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:18.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:18.956][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-17 05:45:18.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-17 05:45:18.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:18.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:18.965][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-17 05:45:18.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-17 05:45:18.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:18.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-17 05:45:18.981][biodb::testThat]
biodb.INFO [2023-10-17 05:45:18.983][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-10-17 05:45:18.986][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:45:18.987][biodb::testThat]
biodb.INFO [2023-10-17 05:45:18.999][biodb::testThat]
biodb.INFO [2023-10-17 05:45:19.000][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-10-17 05:45:19.001][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:45:19.004][biodb::testThat]
biodb.INFO [2023-10-17 05:45:19.016][biodb::testThat]
biodb.INFO [2023-10-17 05:45:19.018][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-10-17 05:45:19.022][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:45:19.023][biodb::testThat]
biodb.DEBUG[2023-10-17 05:45:19.029][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-10-17 05:45:19.967][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-10-17 05:45:20.607][biodb::testThat]
biodb.INFO [2023-10-17 05:45:20.608][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-10-17 05:45:20.613][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:45:20.614][biodb::testThat]
biodb.TRACE[2023-10-17 05:45:20.624][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:20.628][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:20.630][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:20.631][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:20.632][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:20.634][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:20.636][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:20.639][ef$get] fields variable is a list.
biodb.INFO [2023-10-17 05:45:20.642][biodb::testThat]
biodb.INFO [2023-10-17 05:45:20.644][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2023-10-17 05:45:20.646][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:45:20.647][biodb::testThat]
biodb.TRACE[2023-10-17 05:45:20.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:20.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:20.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:20.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:20.687][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:20.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:20.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:20.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:20.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:20.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:20.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:20.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:45:20.828][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-10-17 05:45:20.834][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:45:20.836][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-10-17 05:45:20.838][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:45:20.841][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-10-17 05:45:20.955][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-10-17 05:45:20.960][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:45:20.963][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-10-17 05:45:20.965][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:45:20.969][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-10-17 05:45:20.993][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-17 05:45:20.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-17 05:45:20.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:20.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:21.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:45:21.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:45:21.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:21.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:21.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:21.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:21.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:21.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:21.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:21.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:21.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:21.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:21.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:21.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:21.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:21.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:21.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:21.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:21.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:21.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:21.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:21.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:21.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:21.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:45:21.079][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-10-17 05:45:21.102][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:45:21.104][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:45:21.126][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2023-10-17 05:45:25.604][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2023-10-17 05:45:31.582][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:45:31.586][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2023-10-17 05:45:31.645][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2023-10-17 05:45:33.166][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-10-17 05:45:33.173][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:45:33.174][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:45:33.180][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2023-10-17 05:45:34.091][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2023-10-17 05:45:34.842][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:45:34.845][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2023-10-17 05:45:34.855][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2023-10-17 05:45:34.907][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2023-10-17 05:45:34.913][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:45:34.915][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:45:34.921][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2023-10-17 05:45:35.844][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2023-10-17 05:45:36.666][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:45:36.671][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2023-10-17 05:45:36.681][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2023-10-17 05:45:36.719][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-17 05:45:36.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-17 05:45:36.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:36.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-17 05:45:36.745][biodb::testThat]
biodb.INFO [2023-10-17 05:45:36.746][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-10-17 05:45:36.751][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:45:36.752][biodb::testThat]
biodb.TRACE[2023-10-17 05:45:36.757][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-17 05:45:36.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-17 05:45:36.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:36.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:36.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:45:36.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:45:36.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:36.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:36.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:36.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:36.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:36.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:36.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:36.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:36.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:36.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:36.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:36.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:36.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:36.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:36.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:36.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:36.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:36.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:45:36.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:45:36.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:36.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:36.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:36.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:36.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:36.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:36.846][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-10-17 05:45:36.853][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:45:36.857][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:45:36.862][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2023-10-17 05:45:41.014][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2023-10-17 05:45:46.765][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:45:46.767][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2023-10-17 05:45:46.825][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2023-10-17 05:45:48.275][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-10-17 05:45:48.343][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-10-17 05:45:48.345][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-10-17 05:45:48.348][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-10-17 05:45:48.349][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:45:48.352][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:45:48.353][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-17 05:45:48.354][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:45:48.355][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:45:48.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:45:48.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:48.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:48.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:48.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:48.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:48.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:48.399][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2023-10-17 05:45:48.404][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:45:48.406][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:45:48.409][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2023-10-17 05:45:49.172][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2023-10-17 05:45:50.082][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:45:50.087][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2023-10-17 05:45:50.093][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2023-10-17 05:45:50.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:45:50.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:50.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:50.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:50.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:50.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:50.114][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[2023-10-17 05:45:50.115][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2023-10-17 05:45:50.121][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:45:50.123][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:45:50.125][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2023-10-17 05:45:50.966][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2023-10-17 05:45:51.794][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:45:51.798][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2023-10-17 05:45:51.806][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2023-10-17 05:45:51.809][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2023-10-17 05:45:51.813][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:45:51.814][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-10-17 05:45:51.816][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-17 05:45:51.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:45:51.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:51.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:51.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:51.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:51.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:51.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:45:51.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:51.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:51.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:51.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:51.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:45:51.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:45:51.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:45:51.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:45:51.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.872][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:45:51.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:45:51.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.878][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:45:51.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:45:51.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.889][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:51.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:51.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.894][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:51.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:51.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.899][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:51.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:51.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.907][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:51.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:51.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.913][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:45:51.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:51.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.920][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:45:51.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:51.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.929][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:51.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:51.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.937][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:51.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:51.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:51.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:51.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.953][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:51.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:51.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.960][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:45:51.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:51.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.969][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-17 05:45:51.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:51.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.976][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:51.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:51.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.985][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:51.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:51.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:51.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:51.995][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:45:51.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:51.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.001][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.010][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.026][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:45:52.097][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:45:52.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:52.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:52.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:52.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:52.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:52.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:45:52.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:45:52.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:45:52.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.138][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:45:52.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:45:52.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.144][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:45:52.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:45:52.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.153][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:52.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:52.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.160][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:52.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:45:52.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.167][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:52.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:52.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.177][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:52.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:45:52.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.183][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:45:52.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:52.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.191][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:45:52.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:52.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.198][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:52.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:52.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.204][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:52.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:52.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.216][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:52.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:52.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:52.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:52.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.232][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:45:52.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:52.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.239][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-17 05:45:52.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:52.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.247][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:52.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:52.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:52.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:52.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.261][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:45:52.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:52.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.270][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.276][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.293][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:52.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:52.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:45:52.363][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-10-17 05:45:52.377][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-17 05:45:52.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:45:52.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:52.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:52.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:52.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:52.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:52.394][FUN] Functions in observer BiodbConfig: [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[2023-10-17 05:45:52.397][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.403][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.410][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:45:52.413][private$selectFields]
biodb.TRACE[2023-10-17 05:45:52.414][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:45:52.415][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:45:52.417][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:45:52.419][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.420][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.423][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.424][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.427][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.429][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.430][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.432][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.434][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:45:52.435][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:45:52.437][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.439][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.440][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.442][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.444][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-17 05:45:52.445][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.453][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.459][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.481][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-10-17 05:45:52.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:45:52.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:52.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:52.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:52.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:52.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:52.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:45:52.501][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.506][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.514][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:45:52.515][private$selectFields]
biodb.TRACE[2023-10-17 05:45:52.516][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:45:52.519][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:45:52.520][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:45:52.522][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.524][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.525][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.526][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.530][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.532][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.534][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.536][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.537][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:45:52.540][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:45:52.541][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.570][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.572][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.573][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.577][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-17 05:45:52.579][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.585][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.595][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.602][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-10-17 05:45:52.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:45:52.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:52.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:52.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:52.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:52.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:52.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:45:52.621][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.628][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.632][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:45:52.634][private$selectFields]
biodb.TRACE[2023-10-17 05:45:52.637][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:45:52.638][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:45:52.639][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:45:52.642][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.643][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.644][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.646][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.647][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.649][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.650][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.652][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.653][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:45:52.656][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:45:52.658][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.659][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.662][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.664][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.665][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-17 05:45:52.667][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.673][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.683][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:45:52.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.689][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-10-17 05:45:52.690][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-10-17 05:45:52.693][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-17 05:45:52.707][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-17 05:45:52.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-17 05:45:52.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-17 05:45:52.722][biodb::testThat]
biodb.INFO [2023-10-17 05:45:52.724][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-10-17 05:45:52.725][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:45:52.726][biodb::testThat]
biodb.TRACE[2023-10-17 05:45:52.732][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-17 05:45:52.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-17 05:45:52.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:45:52.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:45:52.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:52.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:52.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:52.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:52.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:52.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:52.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:52.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:52.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:52.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:52.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:45:52.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:45:52.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:52.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:52.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:52.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:52.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:52.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:52.877][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2023-10-17 05:45:52.883][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:45:52.885][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:45:52.890][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2023-10-17 05:45:57.107][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2023-10-17 05:46:02.699][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:46:02.704][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2023-10-17 05:46:02.762][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2023-10-17 05:46:04.177][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-17 05:46:04.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:46:04.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:04.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:04.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:04.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:04.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:04.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:46:04.245][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.254][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.286][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:04.291][private$selectFields]
biodb.TRACE[2023-10-17 05:46:04.292][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:46:04.293][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:46:04.294][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:04.296][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.297][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.298][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.299][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.301][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.302][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.304][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.305][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.306][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:04.325][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:04.329][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.332][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.338][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.340][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.342][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-17 05:46:04.345][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.353][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.359][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.367][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-10-17 05:46:04.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:46:04.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:04.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:04.381][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:04.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:04.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:04.384][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.TRACE[2023-10-17 05:46:04.419][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.427][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.433][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:04.435][private$selectFields]
biodb.TRACE[2023-10-17 05:46:04.437][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:46:04.438][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:46:04.439][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:04.442][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.444][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.446][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.447][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.449][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.451][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.453][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.454][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.455][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:04.457][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:04.458][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.462][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.463][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.465][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.467][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-17 05:46:04.469][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.474][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.484][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.490][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-10-17 05:46:04.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:46:04.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:04.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:04.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:04.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:04.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:04.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:46:04.511][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.547][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.552][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:04.554][private$selectFields]
biodb.TRACE[2023-10-17 05:46:04.555][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:46:04.557][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:46:04.558][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:04.559][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.561][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.562][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.565][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.566][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.567][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.570][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.571][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.573][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:04.575][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:04.576][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.577][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.579][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.580][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.581][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-17 05:46:04.582][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.588][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.595][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:04.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.602][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-10-17 05:46:04.604][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-10-17 05:46:04.605][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-17 05:46:04.616][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-17 05:46:04.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-17 05:46:04.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-17 05:46:04.630][biodb::testThat]
biodb.INFO [2023-10-17 05:46:04.633][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-10-17 05:46:04.635][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:46:04.637][biodb::testThat]
biodb.TRACE[2023-10-17 05:46:04.645][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-17 05:46:04.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-17 05:46:04.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:46:04.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:46:04.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:46:04.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:46:04.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:46:04.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:46:04.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:46:04.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:46:04.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:04.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:46:04.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:46:04.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:04.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:46:04.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:46:04.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:04.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:04.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:04.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:04.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:04.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:04.724][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-10-17 05:46:04.729][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:46:04.731][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-10-17 05:46:04.733][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:46:04.777][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-10-17 05:46:06.429][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-17 05:46:06.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:46:06.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:06.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:06.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:06.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:06.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:06.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:46:06.448][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.453][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.459][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:06.462][private$selectFields]
biodb.TRACE[2023-10-17 05:46:06.463][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:46:06.464][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:46:06.467][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:06.469][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.470][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.473][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.474][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.475][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.478][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.480][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.482][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.484][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:06.485][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:06.487][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.489][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.490][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.491][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.492][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-17 05:46:06.494][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.499][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.509][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.515][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-10-17 05:46:06.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:46:06.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:06.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:06.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:06.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:06.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:06.535][FUN] Functions in observer BiodbConfig: [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[2023-10-17 05:46:06.537][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.546][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.551][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:06.552][private$selectFields]
biodb.TRACE[2023-10-17 05:46:06.554][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:46:06.555][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:46:06.556][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:06.558][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.559][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.561][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.566][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.567][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.568][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.570][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.571][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.572][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:06.574][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:06.575][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.577][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.579][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.580][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.581][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-17 05:46:06.583][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.592][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.598][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.604][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-10-17 05:46:06.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:46:06.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:06.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:06.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:06.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:06.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:06.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:46:06.627][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.635][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.644][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:06.645][private$selectFields]
biodb.TRACE[2023-10-17 05:46:06.646][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:46:06.647][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:46:06.649][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:06.650][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.652][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.653][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.654][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.656][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.659][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.660][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.663][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.665][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:06.666][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:46:06.669][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.671][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.673][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.677][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.678][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-17 05:46:06.680][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.686][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.694][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:06.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:06.701][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-10-17 05:46:06.702][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-10-17 05:46:06.705][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-17 05:46:06.736][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-17 05:46:06.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-17 05:46:06.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:06.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-17 05:46:06.748][biodb::testThat]
biodb.INFO [2023-10-17 05:46:06.749][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2023-10-17 05:46:06.751][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:46:06.752][biodb::testThat]
biodb.DEBUG[2023-10-17 05:46:06.757][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-10-17 05:46:06.758][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:46:06.761][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-10-17 05:46:06.763][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:46:06.764][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:46:06.766][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:46:06.768][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-17 05:46:06.769][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:46:06.771][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:46:06.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:46:06.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:06.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:06.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:06.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:06.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:06.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:06.808][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-10-17 05:46:06.812][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:06.813][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:06.817][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-17 05:46:07.659][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:07.661][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:07.662][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:07.665][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-17 05:46:08.405][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:08.407][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:08.409][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:08.412][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-17 05:46:09.273][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:09.274][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:09.275][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:09.280][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-17 05:46:10.249][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:10.250][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:10.251][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:10.254][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-17 05:46:11.021][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:11.022][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:11.024][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:11.025][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-17 05:46:11.675][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:11.677][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:11.678][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:11.680][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-17 05:46:12.585][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:12.586][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:12.587][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:12.589][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-17 05:46:13.346][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:13.347][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:13.348][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:13.350][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-17 05:46:14.160][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:14.162][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:14.163][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:14.165][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-17 05:46:14.906][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:14.907][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:14.909][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:14.910][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-17 05:46:15.616][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:15.617][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:15.618][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:15.619][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-17 05:46:16.468][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:16.469][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:16.471][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:16.473][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-17 05:46:17.281][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:17.282][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:17.283][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:17.285][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-17 05:46:17.977][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:17.978][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:17.980][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:17.982][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-17 05:46:18.723][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:18.725][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:18.726][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:18.727][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-17 05:46:19.848][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:19.850][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:19.851][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:19.853][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-17 05:46:20.691][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:20.693][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:20.694][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:20.695][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-17 05:46:21.444][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:21.445][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:21.447][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:21.449][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-17 05:46:22.273][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:22.274][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:22.275][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:22.277][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-17 05:46:23.297][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2023-10-17 05:46:23.301][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-10-17 05:46:23.303][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:46:23.307][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:46:23.308][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-17 05:46:23.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:46:23.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:23.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:23.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:23.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:23.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:23.325][FUN] Functions in observer BiodbConfig: [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[2023-10-17 05:46:23.330][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:23.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:23.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:23.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:23.337][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:23.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:23.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:23.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:23.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:23.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:23.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:23.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:23.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:23.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:23.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:23.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:23.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:23.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:23.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:23.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:23.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:23.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:23.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:23.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:23.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:23.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:23.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:23.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:23.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:23.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:23.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:23.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:46:23.372][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-10-17 05:46:23.374][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-10-17 05:46:23.384][biodb::testThat]
biodb.INFO [2023-10-17 05:46:23.386][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-10-17 05:46:23.387][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:46:23.388][biodb::testThat]
biodb.DEBUG[2023-10-17 05:46:23.398][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-10-17 05:46:23.399][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-10-17 05:46:23.401][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-10-17 05:46:23.403][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-10-17 05:46:23.405][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-10-17 05:46:23.406][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:46:23.408][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:46:23.409][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-17 05:46:23.411][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:46:23.412][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:46:23.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:46:23.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:23.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:23.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:23.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:23.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:23.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:23.430][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-10-17 05:46:23.433][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:23.434][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:23.435][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-17 05:46:24.168][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:24.170][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:24.171][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:24.175][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-17 05:46:25.050][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:25.051][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:25.053][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:25.055][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-17 05:46:25.921][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:25.922][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:25.923][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:25.925][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-17 05:46:26.581][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:26.582][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:26.584][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:26.585][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-17 05:46:27.458][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:27.459][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:27.460][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:27.464][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-17 05:46:28.256][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:28.257][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:28.259][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:28.260][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-17 05:46:29.169][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:29.171][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:29.173][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:29.174][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-17 05:46:29.947][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:29.948][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:29.952][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:29.954][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-17 05:46:30.860][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:30.861][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:30.863][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:30.866][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-17 05:46:31.879][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:31.880][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:31.882][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:31.884][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-17 05:46:32.695][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:32.696][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:32.697][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:32.701][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-17 05:46:33.433][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:33.434][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:33.435][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:33.437][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-17 05:46:34.144][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:34.145][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:34.146][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:34.148][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-17 05:46:34.751][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:34.753][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:34.754][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:34.756][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-17 05:46:35.509][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:35.510][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:35.511][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:35.513][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-17 05:46:36.235][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:36.237][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:36.238][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:36.239][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-17 05:46:37.051][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:37.052][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:37.054][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:37.055][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-17 05:46:37.605][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:37.606][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:37.607][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:37.609][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-17 05:46:38.321][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-17 05:46:38.323][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-17 05:46:38.326][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-17 05:46:38.327][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-17 05:46:39.212][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-17 05:46:39.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:46:39.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:39.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:39.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:39.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:39.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:39.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:39.231][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2023-10-17 05:46:39.235][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:39.236][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:39.479][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2023-10-17 05:46:40.237][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2023-10-17 05:46:41.113][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:46:41.117][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2023-10-17 05:46:41.122][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2023-10-17 05:46:41.127][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2023-10-17 05:46:41.130][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:46:41.132][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-10-17 05:46:41.134][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-17 05:46:41.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:46:41.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:41.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:41.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:41.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:41.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:41.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:46:41.153][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:41.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:41.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.161][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:41.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:41.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:46:41.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:46:41.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:41.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:41.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:41.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:41.192][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:41.195][FUN] Functions in observer BiodbConfig: [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[2023-10-17 05:46:41.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:46:41.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:46:41.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:46:41.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:46:41.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.225][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:46:41.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:46:41.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.230][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:46:41.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:46:41.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.236][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:46:41.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:46:41.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.242][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:46:41.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:46:41.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.248][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:46:41.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:46:41.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.252][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:46:41.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:46:41.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.258][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:46:41.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:46:41.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.262][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:46:41.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:46:41.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.269][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:46:41.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:46:41.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.275][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:46:41.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:46:41.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.281][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:46:41.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:46:41.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.286][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:46:41.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:46:41.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:46:41.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:46:41.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:46:41.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:46:41.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.303][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:46:41.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:46:41.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.307][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-17 05:46:41.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:46:41.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:46:41.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:46:41.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.317][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:46:41.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:46:41.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.322][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:46:41.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:46:41.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:46:41.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:46:41.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.331][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:46:41.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:46:41.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:46:41.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:46:41.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:46:41.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:46:41.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:46:41.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:46:41.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.354][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:41.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:41.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.359][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:41.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:41.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.371][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:41.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:46:41.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:41.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:46:41.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:46:41.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:41.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:46:41.438][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-10-17 05:46:41.440][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-10-17 05:46:41.441][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-10-17 05:46:41.459][biodb::testThat]
biodb.INFO [2023-10-17 05:46:41.461][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2023-10-17 05:46:41.462][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:46:41.464][biodb::testThat]
biodb.INFO [2023-10-17 05:46:41.496][biodb::testThat]
biodb.INFO [2023-10-17 05:46:41.497][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2023-10-17 05:46:41.499][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:46:41.500][biodb::testThat]
biodb.INFO [2023-10-17 05:46:41.513][biodb::testThat]
biodb.INFO [2023-10-17 05:46:41.514][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2023-10-17 05:46:41.515][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:46:41.516][biodb::testThat]
biodb.DEBUG[2023-10-17 05:46:41.521][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-10-17 05:46:41.539][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:41.540][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:41.543][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2023-10-17 05:46:45.969][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2023-10-17 05:46:51.222][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:46:51.226][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2023-10-17 05:46:51.275][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2023-10-17 05:46:52.402][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:46:52.404][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:46:52.405][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:52.406][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:46:52.406][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:46:52.407][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:46:52.408][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:46:52.409][ef$get] fields variable is a list.
biodb.INFO [2023-10-17 05:46:52.411][biodb::testThat]
biodb.INFO [2023-10-17 05:46:52.412][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2023-10-17 05:46:52.413][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:46:52.414][biodb::testThat]
biodb.ERROR[2023-10-17 05:46:52.432][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-10-17 05:46:52.452][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-10-17 05:46:52.469][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-17 05:46:52.471][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-10-17 05:46:52.473][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-10-17 05:46:52.474][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-17 05:46:52.476][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:52.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:52.479][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.482][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-10-17 05:46:52.496][biodb::testContext]
biodb.INFO [2023-10-17 05:46:52.497][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:46:52.499][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-10-17 05:46:52.500][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:46:52.501][biodb::testContext]
biodb.INFO [2023-10-17 05:46:52.503][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:46:52.506][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-17 05:46:52.512][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:46:52.514][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-17 05:46:52.516][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-17 05:46:52.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.522][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-17 05:46:52.524][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-17 05:46:52.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.529][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-17 05:46:52.530][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-17 05:46:52.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.535][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-17 05:46:52.536][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-17 05:46:52.537][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-17 05:46:52.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.542][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-17 05:46:52.544][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-17 05:46:52.545][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-17 05:46:52.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.550][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-17 05:46:52.552][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-17 05:46:52.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.556][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-17 05:46:52.558][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-17 05:46:52.560][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-17 05:46:52.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.566][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-17 05:46:52.568][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-17 05:46:52.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.573][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-17 05:46:52.574][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-17 05:46:52.575][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-17 05:46:52.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.580][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:46:52.581][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-17 05:46:52.583][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-17 05:46:52.584][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-17 05:46:52.586][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-17 05:46:52.587][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-17 05:46:52.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.592][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-17 05:46:52.593][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-17 05:46:52.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.597][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-17 05:46:52.598][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-17 05:46:52.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.603][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-17 05:46:52.604][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-17 05:46:52.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.607][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-17 05:46:52.608][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-17 05:46:52.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.612][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-17 05:46:52.613][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-17 05:46:52.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.616][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[2023-10-17 05:46:52.618][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:46:52.620][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-17 05:46:52.636][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-17 05:46:52.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.641][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-17 05:46:52.643][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-17 05:46:52.644][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-17 05:46:52.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.649][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-17 05:46:52.651][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:52.652][self$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[2023-10-17 05:46:52.654][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.655][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:46:52.656][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.657][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:46:52.659][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:52.660][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:46:52.662][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:46:52.664][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:46:52.666][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.667][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-17 05:46:52.668][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:46:52.669][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.671][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.672][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:46:52.672][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:46:52.672][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:46:52.672][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:46:52.672][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:46:52.674][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:46:52.677][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:46:52.678][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:46:52.680][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:46:52.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:46:52.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:46:52.684][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:46:52.685][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.686][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:46:52.688][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:46:52.689][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:52.690][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.692][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-17 05:46:52.694][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:52.695][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:46:52.697][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.698][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:46:52.699][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.700][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:46:52.702][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:52.703][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:46:52.705][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:46:52.707][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:46:52.708][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.709][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-17 05:46:52.710][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:46:52.712][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.714][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.715][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:46:52.715][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:46:52.715][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:46:52.715][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:46:52.715][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:46:52.718][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:46:52.720][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:46:52.721][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:46:52.724][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:46:52.726][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:46:52.727][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:46:52.729][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:46:52.730][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.731][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:46:52.733][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:46:52.734][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:52.735][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.737][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-17 05:46:52.739][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.741][self$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[2023-10-17 05:46:52.742][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.744][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:46:52.745][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.746][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:46:52.748][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:52.750][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:46:52.752][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:46:52.753][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:46:52.754][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:52.756][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-17 05:46:52.757][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:46:52.760][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.762][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.763][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.764][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:46:52.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:46:52.788][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:46:52.789][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:46:52.790][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:46:52.791][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:46:52.792][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:46:52.793][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.794][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:46:52.795][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:46:52.796][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:52.797][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.799][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-17 05:46:52.801][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.802][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:46:52.804][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.805][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:46:52.806][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.808][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:46:52.809][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:52.810][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:46:52.811][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:46:52.813][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:46:52.814][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:52.816][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-17 05:46:52.818][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:46:52.819][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.820][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:52.821][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.823][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:46:52.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:46:52.826][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:46:52.828][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:46:52.830][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:46:52.831][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:46:52.832][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:46:52.834][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.835][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:46:52.836][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:46:52.837][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:52.839][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:52.840][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:46:52.842][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.843][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[2023-10-17 05:46:52.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.854][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[2023-10-17 05:46:52.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.898][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[2023-10-17 05:46:52.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.911][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[2023-10-17 05:46:52.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.930][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[2023-10-17 05:46:52.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:52.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:52.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:52.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:52.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:52.947][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[2023-10-17 05:46:52.948][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-17 05:46:52.950][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-17 05:46:52.951][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-17 05:46:52.953][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-17 05:46:52.954][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-17 05:46:52.956][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-17 05:46:52.957][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-17 05:46:52.959][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-17 05:46:52.960][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-17 05:46:52.962][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-17 05:46:52.963][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-17 05:46:52.965][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-17 05:46:52.966][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-17 05:46:52.969][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-17 05:46:52.971][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-17 05:46:52.973][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-17 05:46:52.975][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-17 05:46:52.976][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-17 05:46:52.979][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-17 05:46:52.981][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-17 05:46:52.984][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-17 05:46:52.986][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-17 05:46:52.988][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-17 05:46:52.990][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-17 05:46:52.992][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-17 05:46:52.993][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-17 05:46:52.995][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-17 05:46:52.997][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-17 05:46:52.999][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-17 05:46:53.001][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-17 05:46:53.003][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-17 05:46:53.005][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-17 05:46:53.007][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-17 05:46:53.009][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-17 05:46:53.011][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-17 05:46:53.013][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-17 05:46:53.015][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-17 05:46:53.017][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-17 05:46:53.019][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-17 05:46:53.021][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-17 05:46:53.023][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-17 05:46:53.026][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-17 05:46:53.028][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-17 05:46:53.030][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-17 05:46:53.032][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-17 05:46:53.034][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-17 05:46:53.036][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-17 05:46:53.038][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-17 05:46:53.040][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-17 05:46:53.042][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-17 05:46:53.043][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-17 05:46:53.045][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-17 05:46:53.047][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-17 05:46:53.049][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-17 05:46:53.050][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-17 05:46:53.052][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-17 05:46:53.054][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-17 05:46:53.056][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-17 05:46:53.059][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-17 05:46:53.061][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-17 05:46:53.063][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-17 05:46:53.065][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-17 05:46:53.067][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-17 05:46:53.070][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-17 05:46:53.072][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-17 05:46:53.074][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-17 05:46:53.076][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-17 05:46:53.078][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-17 05:46:53.080][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-17 05:46:53.082][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-17 05:46:53.083][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-17 05:46:53.085][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-17 05:46:53.087][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-17 05:46:53.089][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-17 05:46:53.091][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-17 05:46:53.093][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-17 05:46:53.095][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-17 05:46:53.097][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-17 05:46:53.100][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-17 05:46:53.102][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-17 05:46:53.103][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-17 05:46:53.105][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-17 05:46:53.107][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-17 05:46:53.109][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-17 05:46:53.112][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:46:53.114][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:46:53.116][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.118][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.232][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[2023-10-17 05:46:53.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.268][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[2023-10-17 05:46:53.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.284][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[2023-10-17 05:46:53.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:46:53.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:46:53.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:46:53.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:46:53.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:46:53.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:46:53.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:46:53.294][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-10-17 05:46:53.297][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-10-17 05:46:53.300][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:53.301][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-10-17 05:46:53.302][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:53.304][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:46:53.305][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:53.308][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:46:53.309][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:53.311][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:46:53.312][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:46:53.314][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:46:53.315][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:53.317][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-10-17 05:46:53.318][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:46:53.319][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-10-17 05:46:53.319][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-10-17 05:46:53.319][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-10-17 05:46:53.319][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-10-17 05:46:53.319][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-10-17 05:46:53.319][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-10-17 05:46:53.319][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-10-17 05:46:53.319][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-10-17 05:46:53.319][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-10-17 05:46:53.321][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-17 05:46:53.322][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:46:53.322][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:46:53.323][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:46:53.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:46:53.325][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:46:53.326][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:46:53.327][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:46:53.328][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:46:53.330][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:46:53.331][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-17 05:46:53.331][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-10-17 05:46:53.332][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:46:53.333][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:46:53.334][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-17 05:46:53.336][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:46:53.337][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-10-17 05:46:53.339][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-17 05:46:53.342][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-10-17 05:46:53.344][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-10-17 05:46:53.346][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-10-17 05:46:53.347][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-10-17 05:46:53.349][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-17 05:46:53.350][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-17 05:46:53.351][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-10-17 05:46:53.353][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-10-17 05:46:53.354][biodb::testThat]
biodb.INFO [2023-10-17 05:46:53.356][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-10-17 05:46:53.357][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:46:53.358][biodb::testThat]
biodb.DEBUG[2023-10-17 05:46:53.363][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2023-10-17 05:46:53.369][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:53.370][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:53.372][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-10-17 05:46:54.241][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2023-10-17 05:46:55.150][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:46:55.153][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-10-17 05:46:55.159][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-10-17 05:46:55.172][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2023-10-17 05:46:55.176][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:55.178][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:55.197][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2023-10-17 05:46:55.988][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2023-10-17 05:46:56.880][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:46:56.884][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2023-10-17 05:46:56.889][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2023-10-17 05:46:56.903][biodb::testThat]
biodb.INFO [2023-10-17 05:46:56.905][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-10-17 05:46:56.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:46:56.907][biodb::testThat]
biodb.INFO [2023-10-17 05:46:56.942][biodb::testThat]
biodb.INFO [2023-10-17 05:46:56.943][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-10-17 05:46:56.944][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:46:56.945][biodb::testThat]
biodb.DEBUG[2023-10-17 05:46:56.975][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-10-17 05:46:56.979][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:56.980][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:56.982][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-10-17 05:46:57.701][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-10-17 05:46:58.431][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:46:58.434][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-10-17 05:46:58.439][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-10-17 05:46:58.445][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-10-17 05:46:58.449][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:46:58.451][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-10-17 05:46:58.454][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:46:58.456][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-10-17 05:46:58.462][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2023-10-17 05:46:58.467][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:58.469][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:58.475][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-10-17 05:46:59.166][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2023-10-17 05:46:59.777][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:46:59.780][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-10-17 05:46:59.786][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-10-17 05:46:59.795][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2023-10-17 05:46:59.800][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:46:59.801][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:46:59.804][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-10-17 05:47:01.218][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-10-17 05:47:02.773][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:47:02.776][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-10-17 05:47:02.788][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-10-17 05:47:02.958][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2023-10-17 05:47:02.963][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:47:02.964][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:47:02.968][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2023-10-17 05:47:04.372][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2023-10-17 05:47:06.192][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:47:06.195][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2023-10-17 05:47:06.211][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2023-10-17 05:47:06.399][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-17 05:47:06.401][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-10-17 05:47:06.402][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-10-17 05:47:06.404][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-17 05:47:06.405][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:06.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:06.407][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.409][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-10-17 05:47:06.415][biodb::testContext]
biodb.INFO [2023-10-17 05:47:06.416][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:47:06.417][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-10-17 05:47:06.418][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:47:06.420][biodb::testContext]
biodb.INFO [2023-10-17 05:47:06.422][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:47:06.424][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-17 05:47:06.429][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:47:06.431][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-17 05:47:06.433][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-17 05:47:06.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.438][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-17 05:47:06.439][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-17 05:47:06.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.445][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-17 05:47:06.447][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-17 05:47:06.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.452][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-17 05:47:06.454][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-17 05:47:06.455][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-17 05:47:06.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.462][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-17 05:47:06.464][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-17 05:47:06.465][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-17 05:47:06.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.470][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-17 05:47:06.471][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-17 05:47:06.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.476][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-17 05:47:06.478][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-17 05:47:06.479][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-17 05:47:06.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.485][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-17 05:47:06.486][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-17 05:47:06.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.493][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-17 05:47:06.494][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-17 05:47:06.495][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-17 05:47:06.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.499][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:47:06.501][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-17 05:47:06.502][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-17 05:47:06.503][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-17 05:47:06.504][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-17 05:47:06.506][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-17 05:47:06.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.510][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-17 05:47:06.511][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-17 05:47:06.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.518][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-17 05:47:06.521][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-17 05:47:06.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.527][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-17 05:47:06.530][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-17 05:47:06.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.539][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-17 05:47:06.540][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-17 05:47:06.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.546][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-17 05:47:06.547][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-17 05:47:06.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.552][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:47:06.554][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-17 05:47:06.571][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-17 05:47:06.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.576][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-17 05:47:06.577][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-17 05:47:06.578][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-17 05:47:06.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.583][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-17 05:47:06.585][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:06.586][self$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[2023-10-17 05:47:06.587][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.588][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:47:06.590][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.592][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:47:06.594][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:06.596][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:47:06.598][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:47:06.599][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:47:06.601][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.602][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-17 05:47:06.604][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:47:06.605][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.606][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.610][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:47:06.610][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:47:06.610][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:47:06.610][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:47:06.610][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:47:06.612][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:47:06.613][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:47:06.614][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:47:06.616][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:47:06.617][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:47:06.620][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:47:06.621][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:47:06.622][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.624][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:47:06.625][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:47:06.627][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:06.628][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.630][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-17 05:47:06.633][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:06.634][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:47:06.636][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.637][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:47:06.638][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.640][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:47:06.642][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:06.644][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:47:06.647][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:47:06.648][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:47:06.650][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.652][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-17 05:47:06.654][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:47:06.655][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.657][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.658][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:47:06.658][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:47:06.658][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:47:06.658][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:47:06.658][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:47:06.659][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:47:06.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:47:06.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:47:06.664][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:47:06.665][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:47:06.666][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:47:06.705][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:47:06.707][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.708][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:47:06.710][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:47:06.712][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:06.714][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.716][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-17 05:47:06.718][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.720][self$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[2023-10-17 05:47:06.722][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.724][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:47:06.725][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.726][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:47:06.728][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:06.729][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:47:06.731][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:47:06.733][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:47:06.735][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:06.737][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-17 05:47:06.738][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:47:06.740][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.742][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.743][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.744][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:47:06.746][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:47:06.747][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:47:06.749][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:47:06.751][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:47:06.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:47:06.753][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:47:06.755][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.756][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:47:06.757][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:47:06.759][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:06.760][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.761][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-17 05:47:06.764][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.766][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:47:06.768][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.770][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:47:06.771][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.772][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:47:06.773][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:06.775][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:47:06.776][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:47:06.777][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:47:06.778][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:06.779][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-17 05:47:06.780][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:47:06.781][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.782][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:06.784][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.785][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:47:06.786][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:47:06.787][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:47:06.788][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:47:06.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:47:06.790][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:47:06.791][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:47:06.792][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.793][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:47:06.794][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:47:06.795][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:06.796][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:06.797][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:47:06.798][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:06.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:06.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:06.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:06.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:06.930][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[2023-10-17 05:47:06.932][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-17 05:47:06.934][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-17 05:47:06.937][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-17 05:47:06.941][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-17 05:47:06.943][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-17 05:47:06.946][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-17 05:47:06.948][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-17 05:47:06.950][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-17 05:47:06.952][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-17 05:47:06.954][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-17 05:47:06.956][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-17 05:47:06.958][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-17 05:47:06.960][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-17 05:47:06.962][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-17 05:47:06.965][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-17 05:47:06.967][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-17 05:47:06.968][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-17 05:47:06.970][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-17 05:47:06.972][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-17 05:47:06.974][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-17 05:47:06.976][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-17 05:47:06.978][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-17 05:47:06.980][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-17 05:47:06.982][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-17 05:47:06.984][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-17 05:47:06.985][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-17 05:47:06.987][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-17 05:47:06.988][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-17 05:47:06.990][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-17 05:47:06.991][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-17 05:47:06.993][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-17 05:47:06.995][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-17 05:47:06.996][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-17 05:47:06.998][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-17 05:47:06.999][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-17 05:47:07.001][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-17 05:47:07.004][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-17 05:47:07.007][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-17 05:47:07.009][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-17 05:47:07.011][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-17 05:47:07.014][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-17 05:47:07.016][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-17 05:47:07.018][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-17 05:47:07.020][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-17 05:47:07.022][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-17 05:47:07.024][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-17 05:47:07.026][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-17 05:47:07.028][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-17 05:47:07.030][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-17 05:47:07.032][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-17 05:47:07.034][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-17 05:47:07.037][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-17 05:47:07.039][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-17 05:47:07.041][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-17 05:47:07.043][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-17 05:47:07.045][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-17 05:47:07.047][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-17 05:47:07.050][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-17 05:47:07.052][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-17 05:47:07.054][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-17 05:47:07.056][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-17 05:47:07.058][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-17 05:47:07.060][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-17 05:47:07.062][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-17 05:47:07.064][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-17 05:47:07.066][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-17 05:47:07.068][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-17 05:47:07.070][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-17 05:47:07.072][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-17 05:47:07.073][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-17 05:47:07.075][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-17 05:47:07.077][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-17 05:47:07.080][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-17 05:47:07.082][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-17 05:47:07.084][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-17 05:47:07.086][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-17 05:47:07.088][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-17 05:47:07.110][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-17 05:47:07.112][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-17 05:47:07.113][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-17 05:47:07.117][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-17 05:47:07.118][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-17 05:47:07.123][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-17 05:47:07.125][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-17 05:47:07.128][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:47:07.129][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:47:07.130][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.133][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.166][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[2023-10-17 05:47:07.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.176][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[2023-10-17 05:47:07.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.208][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.DEBUG[2023-10-17 05:47:07.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:47:07.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:07.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:07.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:07.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:07.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:07.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:47:07.287][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-10-17 05:47:07.290][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-10-17 05:47:07.293][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:07.295][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-10-17 05:47:07.297][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:07.298][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:47:07.300][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:07.301][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:47:07.302][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:07.303][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:47:07.305][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:47:07.306][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:47:07.308][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:07.309][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-10-17 05:47:07.310][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:47:07.311][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-10-17 05:47:07.311][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-10-17 05:47:07.311][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-10-17 05:47:07.311][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-10-17 05:47:07.311][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-10-17 05:47:07.311][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-10-17 05:47:07.311][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-10-17 05:47:07.311][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-10-17 05:47:07.311][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-10-17 05:47:07.313][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-17 05:47:07.315][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:47:07.315][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:47:07.316][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:47:07.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:47:07.318][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:47:07.320][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:47:07.321][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:47:07.322][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:47:07.324][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:47:07.326][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-17 05:47:07.326][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-10-17 05:47:07.327][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:47:07.328][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:47:07.329][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-17 05:47:07.331][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:47:07.333][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-10-17 05:47:07.335][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-17 05:47:07.340][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-10-17 05:47:07.341][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-10-17 05:47:07.343][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-10-17 05:47:07.345][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-10-17 05:47:07.347][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-17 05:47:07.348][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-17 05:47:07.350][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-10-17 05:47:07.351][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-10-17 05:47:07.353][biodb::testThat]
biodb.INFO [2023-10-17 05:47:07.354][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2023-10-17 05:47:07.355][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:47:07.356][biodb::testThat]
biodb.DEBUG[2023-10-17 05:47:07.361][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-10-17 05:47:07.367][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:47:07.369][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-10-17 05:47:07.371][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:47:07.411][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-10-17 05:47:08.888][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-10-17 05:47:08.890][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-10-17 05:47:08.892][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-10-17 05:47:08.896][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-10-17 05:47:08.899][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2023-10-17 05:47:08.901][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:47:08.903][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-10-17 05:47:08.905][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-17 05:47:08.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:47:08.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:08.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:08.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:08.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:08.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:08.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:47:08.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:08.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:08.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:08.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:08.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:08.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:08.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:08.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:08.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:08.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:08.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:08.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:08.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:08.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:08.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:08.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:08.955][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:47:08.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:47:08.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:08.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:08.962][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:47:08.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:47:08.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:08.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:08.969][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:08.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:08.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:08.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:08.978][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:08.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:08.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:08.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:08.985][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:08.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:08.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:08.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:08.992][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:08.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:08.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:08.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:08.999][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:47:09.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.009][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:47:09.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.016][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:09.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:09.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.023][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:09.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:09.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.043][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:47:09.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.049][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-17 05:47:09.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.055][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.062][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.069][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:47:09.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.077][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.101][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.110][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.117][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.130][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:47:09.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:47:09.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:09.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:09.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:09.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:09.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:09.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:47:09.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.217][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:47:09.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-17 05:47:09.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.223][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:47:09.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:47:09.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.231][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.239][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.246][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.257][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.265][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:47:09.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.272][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-17 05:47:09.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.279][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:09.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:09.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.285][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:09.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:09.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.292][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.299][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.308][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:47:09.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.314][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-17 05:47:09.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.335][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-17 05:47:09.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.342][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.395][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.409][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:47:09.483][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-10-17 05:47:09.487][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-17 05:47:09.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:47:09.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:09.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:09.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:09.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:09.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:09.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:47:09.509][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:47:09.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:47:09.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.516][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:47:09.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:47:09.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.524][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-17 05:47:09.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-17 05:47:09.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.532][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-17 05:47:09.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-17 05:47:09.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.540][private$selectFields] Fields none
biodb.TRACE[2023-10-17 05:47:09.542][private$selectFields]
biodb.TRACE[2023-10-17 05:47:09.544][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-10-17 05:47:09.545][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:47:09.546][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:47:09.547][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.550][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.551][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.553][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.557][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.559][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.563][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.564][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.565][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.569][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.570][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.573][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.574][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.576][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.578][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.579][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.582][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.583][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.585][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.588][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.589][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:09.591][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:09.593][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.594][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.595][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.596][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.598][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.599][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.600][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.603][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.604][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.605][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.609][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.610][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.611][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.613][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.614][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.616][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.617][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.619][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.620][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.621][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.623][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.625][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.626][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.628][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.630][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.631][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.633][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.635][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.636][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.639][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.641][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:09.644][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:09.646][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.647][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.650][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.652][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.654][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.655][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.656][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.657][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.659][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.660][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.662][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:47:09.666][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:47:09.667][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.668][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.671][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.672][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.674][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.675][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.677][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.679][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.681][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.685][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.686][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.688][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.690][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.692][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.695][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.697][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.699][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.700][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.701][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.702][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.707][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:09.708][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:09.711][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.712][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.713][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.715][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.716][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.717][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.719][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.724][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.725][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.727][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.729][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-10-17 05:47:09.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:09.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:09.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:09.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.776][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.783][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.790][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:09.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.798][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.806][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.812][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:09.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:09.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.838][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:09.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:09.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.843][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:09.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:09.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.851][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:09.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:09.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.892][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:09.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:09.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.910][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.919][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.924][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:09.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.940][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2023-10-17 05:47:09.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:47:09.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:09.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:09.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:09.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:09.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:09.960][FUN] Functions in observer BiodbConfig: [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[2023-10-17 05:47:09.964][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:47:09.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:47:09.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.970][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:47:09.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:47:09.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.978][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-17 05:47:09.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-17 05:47:09.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.986][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-17 05:47:09.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-17 05:47:09.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:09.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:09.994][private$selectFields] Fields none
biodb.TRACE[2023-10-17 05:47:09.995][private$selectFields]
biodb.TRACE[2023-10-17 05:47:09.996][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-10-17 05:47:09.998][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:47:10.000][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:47:10.002][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:10.003][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:10.007][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.009][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.011][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:10.013][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:10.014][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.016][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.017][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:10.018][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:10.020][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.021][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.023][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:10.027][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:10.028][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.030][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.032][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:10.034][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:10.035][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.037][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.039][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:10.040][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:10.042][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.043][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.044][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:10.045][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:10.047][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.048][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.052][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:10.054][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:10.055][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.057][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.058][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:10.059][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:10.061][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.062][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.063][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:10.064][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:10.066][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.067][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.068][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:10.071][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:10.072][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.073][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.075][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:10.078][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:10.080][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.083][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.085][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:10.086][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:10.090][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.091][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.093][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:10.095][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:10.097][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.099][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.100][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:10.103][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:10.105][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.106][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.110][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:10.111][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:10.113][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.114][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.115][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:47:10.118][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-17 05:47:10.119][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:10.120][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:10.122][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.124][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.125][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:10.128][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:10.130][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.131][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.133][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:10.136][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:10.139][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.140][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.142][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:10.145][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:10.147][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.149][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.151][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:10.152][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:10.156][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.157][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.160][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:10.162][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:10.163][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.165][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.167][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:10.169][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:10.170][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.171][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.173][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:10.176][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:10.178][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.181][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.183][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-10-17 05:47:10.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:10.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:10.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:10.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:10.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:47:10.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:47:10.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:10.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:10.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:10.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:10.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:47:10.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:47:10.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.233][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:10.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:10.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.238][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:10.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:10.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.248][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:10.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-17 05:47:10.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.257][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:10.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:10.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.264][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:10.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:10.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.272][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:10.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-17 05:47:10.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:10.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:10.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:10.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:10.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:10.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:47:10.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.303][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:10.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:10.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.309][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:10.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:10.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.315][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:47:10.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:47:10.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.324][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:10.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:10.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.330][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:10.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:10.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:47:10.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:47:10.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.346][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:10.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:10.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.356][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:10.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:10.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.362][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:10.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-17 05:47:10.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:47:10.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:47:10.374][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2023-10-17 05:47:10.377][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-10-17 05:47:10.406][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-10-17 05:47:10.417][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-17 05:47:10.419][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-10-17 05:47:10.421][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-10-17 05:47:10.422][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-17 05:47:10.424][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:47:10.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:47:10.426][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:47:10.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:47:10.430][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:47:10.431][FUN] Functions in observer 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 168 ]
> 
> proc.time()
   user  system elapsed 
 25.204   1.908 119.158

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn2.6140.7285.647
LipidmapsStructureEntry0.3850.0140.414