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This page was generated on 2023-10-16 11:36:52 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 14:00:13 -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)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for biodbLipidmaps on merida1


To the developers/maintainers of the biodbLipidmaps package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: 2023-10-15 23:07:23 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 23:10:47 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 204.6 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/meat/biodbLipidmaps.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* 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 4.085  1.123   7.351
* 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-x86_64/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: x86_64-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 [2023-10-15 23:09:11.807][biodb::testContext]
biodb.INFO [2023-10-15 23:09:11.814][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-15 23:09:11.817][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-10-15 23:09:11.819][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-15 23:09:11.822][biodb::testContext]
biodb.INFO [2023-10-15 23:09:11.839][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-15 23:09:11.844][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-15 23:09:11.867][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 23:09:11.870][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-15 23:09:11.875][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-15 23:09:11.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:11.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:11.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:11.886][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-15 23:09:11.958][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-15 23:09:11.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:11.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:11.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:11.971][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-15 23:09:11.978][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-15 23:09:11.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:11.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:11.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:11.991][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-15 23:09:11.993][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-15 23:09:11.996][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-15 23:09:11.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.013][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-15 23:09:12.016][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-15 23:09:12.019][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-15 23:09:12.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.033][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-15 23:09:12.040][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-15 23:09:12.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.053][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-15 23:09:12.055][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-15 23:09:12.058][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-15 23:09:12.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.072][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-15 23:09:12.075][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-15 23:09:12.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.085][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-15 23:09:12.089][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-15 23:09:12.092][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-15 23:09:12.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.106][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-15 23:09:12.109][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-15 23:09:12.115][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-15 23:09:12.118][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-15 23:09:12.120][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-15 23:09:12.126][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-15 23:09:12.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.133][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.DEBUG[2023-10-15 23:09:12.138][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-15 23:09:12.142][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-15 23:09:12.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.156][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-15 23:09:12.159][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-15 23:09:12.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.171][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-15 23:09:12.176][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-15 23:09:12.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.188][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-15 23:09:12.191][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-15 23:09:12.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.204][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-15 23:09:12.209][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-15 23:09:12.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.221][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-15 23:09:12.224][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-15 23:09:12.251][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-15 23:09:12.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.265][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-15 23:09:12.268][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-15 23:09:12.273][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-15 23:09:12.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.295][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-15 23:09:12.421][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:12.488][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-15 23:09:12.490][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.492][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:09:12.495][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.497][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:09:12.502][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:12.504][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:09:12.506][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 23:09:12.508][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:09:12.514][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.516][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-15 23:09:12.518][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:09:12.520][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.522][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.527][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 23:09:12.527][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 23:09:12.527][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-15 23:09:12.527][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-15 23:09:12.527][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-15 23:09:12.529][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:09:12.532][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:09:12.534][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:09:12.539][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:09:12.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:09:12.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:09:12.545][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:09:12.547][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.554][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:09:12.556][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:09:12.558][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:12.560][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.562][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-15 23:09:12.570][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:12.572][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-15 23:09:12.574][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.578][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:09:12.580][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.583][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:09:12.585][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:12.587][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:09:12.593][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-15 23:09:12.596][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:09:12.598][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.600][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-15 23:09:12.605][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:09:12.607][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.610][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.612][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 23:09:12.612][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 23:09:12.612][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-15 23:09:12.612][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-15 23:09:12.612][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-15 23:09:12.617][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:09:12.620][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:09:12.622][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:09:12.624][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:09:12.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:09:12.631][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:09:12.634][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:09:12.636][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.638][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:09:12.642][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:09:12.645][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:12.647][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.650][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-15 23:09:12.655][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.658][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-15 23:09:12.661][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.664][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:09:12.666][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.671][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:09:12.673][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:12.675][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:09:12.682][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 23:09:12.684][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:09:12.686][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:12.688][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-15 23:09:12.694][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:09:12.697][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.700][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.702][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.707][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:09:12.710][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:09:12.712][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:09:12.714][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:09:12.718][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:09:12.721][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:09:12.723][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:09:12.725][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.727][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:09:12.733][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:09:12.735][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:12.737][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.740][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-15 23:09:12.746][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.748][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-15 23:09:12.751][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.756][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:09:12.759][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.761][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:09:12.763][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:12.765][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:09:12.771][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-15 23:09:12.773][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:09:12.775][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:12.778][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-15 23:09:12.784][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:09:12.786][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.790][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:12.793][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.797][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:09:12.799][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:09:12.801][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:09:12.803][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:09:12.808][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:09:12.811][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:09:12.813][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:09:12.815][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.819][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:09:12.822][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:09:12.824][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:12.826][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:12.838][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 23:09:12.840][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:12.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:12.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:12.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:12.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.871][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[2023-10-15 23:09:12.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:12.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:12.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:12.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:12.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.900][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[2023-10-15 23:09:12.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:12.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:12.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.914][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[2023-10-15 23:09:12.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:12.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:12.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:12.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:12.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.941][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[2023-10-15 23:09:12.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:12.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:12.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:12.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:12.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:12.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:12.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:12.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:12.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:12.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:12.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:12.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.042][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[2023-10-15 23:09:13.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.089][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-15 23:09:13.102][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-15 23:09:13.106][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-15 23:09:13.115][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-15 23:09:13.118][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-15 23:09:13.121][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-15 23:09:13.128][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-15 23:09:13.133][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-15 23:09:13.139][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-15 23:09:13.155][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-15 23:09:13.159][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-15 23:09:13.162][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-15 23:09:13.171][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-15 23:09:13.175][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-15 23:09:13.178][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-15 23:09:13.185][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-15 23:09:13.189][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-15 23:09:13.193][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-15 23:09:13.205][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-15 23:09:13.209][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-15 23:09:13.212][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-15 23:09:13.217][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-15 23:09:13.222][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-15 23:09:13.233][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-15 23:09:13.237][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-15 23:09:13.240][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-15 23:09:13.247][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-15 23:09:13.262][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-15 23:09:13.265][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-15 23:09:13.273][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-15 23:09:13.276][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-15 23:09:13.279][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-15 23:09:13.286][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-15 23:09:13.290][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-15 23:09:13.299][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-15 23:09:13.302][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-15 23:09:13.305][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-15 23:09:13.314][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-15 23:09:13.319][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-15 23:09:13.323][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-15 23:09:13.331][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-15 23:09:13.336][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-15 23:09:13.339][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-15 23:09:13.346][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-15 23:09:13.349][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-15 23:09:13.353][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-15 23:09:13.362][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-15 23:09:13.366][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-15 23:09:13.369][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-15 23:09:13.374][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-15 23:09:13.377][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-15 23:09:13.380][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-15 23:09:13.390][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-15 23:09:13.394][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-15 23:09:13.397][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-15 23:09:13.406][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-15 23:09:13.409][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-15 23:09:13.412][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-15 23:09:13.416][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-15 23:09:13.419][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-15 23:09:13.422][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-15 23:09:13.429][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-15 23:09:13.432][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-15 23:09:13.436][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-15 23:09:13.465][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-15 23:09:13.468][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-15 23:09:13.471][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-15 23:09:13.487][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-15 23:09:13.490][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-15 23:09:13.493][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-15 23:09:13.499][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-15 23:09:13.504][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-15 23:09:13.507][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-15 23:09:13.518][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-15 23:09:13.522][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-15 23:09:13.526][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-15 23:09:13.532][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-15 23:09:13.536][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-15 23:09:13.541][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-15 23:09:13.551][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-15 23:09:13.554][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-15 23:09:13.558][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-15 23:09:13.561][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-15 23:09:13.577][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-15 23:09:13.580][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-15 23:09:13.587][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 23:09:13.589][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.596][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.806][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[2023-10-15 23:09:13.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.839][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[2023-10-15 23:09:13.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:09:13.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:13.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:13.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:13.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:13.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:13.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:13.918][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-10-15 23:09:13.949][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 23:09:13.954][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:13.960][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-10-15 23:09:13.963][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:13.967][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:09:13.975][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:13.978][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:09:13.986][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:13.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:09:13.991][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 23:09:13.995][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:09:14.001][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:14.004][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-10-15 23:09:14.006][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:09:14.009][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-10-15 23:09:14.009][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-10-15 23:09:14.009][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-10-15 23:09:14.009][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-10-15 23:09:14.009][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-10-15 23:09:14.009][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-10-15 23:09:14.009][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-10-15 23:09:14.009][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-10-15 23:09:14.009][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-10-15 23:09:14.015][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-15 23:09:14.017][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 23:09:14.017][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 23:09:14.020][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:09:14.022][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:09:14.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:09:14.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:09:14.036][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:09:14.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:09:14.047][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:09:14.049][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-15 23:09:14.049][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-10-15 23:09:14.052][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:09:14.067][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:09:14.069][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-15 23:09:14.072][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:09:14.091][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-10-15 23:09:14.095][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-15 23:09:14.175][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 23:09:14.183][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-10-15 23:09:14.197][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 23:09:14.206][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-10-15 23:09:14.220][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-15 23:09:14.225][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-15 23:09:14.229][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-10-15 23:09:14.231][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-10-15 23:09:14.260][biodb::testThat]
biodb.INFO [2023-10-15 23:09:14.262][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-10-15 23:09:14.264][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:14.270][biodb::testThat]
biodb.TRACE[2023-10-15 23:09:14.280][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2023-10-15 23:09:14.288][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-10-15 23:09:14.296][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-15 23:09:14.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:14.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:14.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:14.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:14.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:14.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:14.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:09:14.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:14.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:14.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:14.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:14.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:09:14.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:09:14.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.506][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:09:14.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:09:14.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.518][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:09:14.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:09:14.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.531][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:14.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:14.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.627][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:14.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:14.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.641][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:14.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:14.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.656][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:14.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:14.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.666][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:09:14.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:14.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.680][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:09:14.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:14.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.695][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:14.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:14.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:14.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:14.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.720][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:14.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:14.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:14.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:14.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.746][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:09:14.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:14.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.758][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 23:09:14.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:14.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:14.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:14.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:14.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:14.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.795][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:09:14.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:14.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:14.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:14.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:14.881][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:14.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:14.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:14.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.024][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:15.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:15.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:15.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:15.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.047][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:15.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:15.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.061][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.077][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.109][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:09:15.219][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-10-15 23:09:15.231][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 23:09:15.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 23:09:15.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.244][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 23:09:15.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 23:09:15.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.255][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-15 23:09:15.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-15 23:09:15.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.271][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-15 23:09:15.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-15 23:09:15.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.376][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.480][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.493][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.505][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:15.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.571][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.576][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.589][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.591][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:15.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:15.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:15.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:15.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.640][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:15.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:15.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:15.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:15.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.661][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:15.664][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:15.666][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.668][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:15.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:15.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.707][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:15.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:15.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.717][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:15.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:15.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.727][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:15.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:15.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.739][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:15.741][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:15.747][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.749][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.752][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:15.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:15.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.788][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:15.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:15.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.800][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:15.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:15.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.811][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:15.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:15.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.824][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:15.826][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:15.828][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.830][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.834][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:15.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:15.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:15.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:15.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:15.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:15.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:15.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:15.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.896][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:15.899][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:15.901][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.904][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:15.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:15.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.944][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:15.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:15.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.956][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:15.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:15.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.968][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:15.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:15.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.981][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:15.984][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:15.986][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:15.990][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:15.992][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:15.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:15.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.031][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:16.034][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:16.036][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.038][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.057][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:16.060][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:16.062][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.064][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.084][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:16.086][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:16.088][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.090][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.107][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:16.112][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:16.114][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.116][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.131][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:16.136][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:16.138][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.140][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.156][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:16.161][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:16.163][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.165][ef$get] fields variable is a list.
biodb.INFO [2023-10-15 23:09:16.227][biodb::testThat]
biodb.INFO [2023-10-15 23:09:16.230][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-10-15 23:09:16.236][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:16.238][biodb::testThat]
biodb.DEBUG[2023-10-15 23:09:16.279][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-10-15 23:09:16.298][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-15 23:09:16.305][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-10-15 23:09:16.310][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:09:16.313][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-10-15 23:09:16.315][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-15 23:09:16.390][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-10-15 23:09:16.393][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-15 23:09:16.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:16.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:16.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:16.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:16.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:16.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:16.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:09:16.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:16.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:16.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:16.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:16.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:09:16.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:09:16.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:09:16.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:09:16.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.491][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:09:16.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:09:16.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.512][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:09:16.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:09:16.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.529][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:16.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:16.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.543][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:16.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:16.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.568][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:16.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:16.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.586][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:16.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:16.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.605][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:09:16.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:16.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.615][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:09:16.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:16.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.638][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:16.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:16.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.654][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:16.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:16.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:16.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:16.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.685][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:16.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:16.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.698][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:09:16.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:16.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.707][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 23:09:16.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:16.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:16.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:16.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.736][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:16.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:16.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.749][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:09:16.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:16.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:16.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:16.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:16.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:16.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:16.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:16.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:16.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:16.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:16.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:16.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.825][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:16.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:16.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.841][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:16.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:16.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:16.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:16.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.862][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:16.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:16.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:16.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:16.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:16.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:16.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:16.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:16.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:16.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:16.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:16.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:16.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:16.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:16.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:09:16.949][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-10-15 23:09:16.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-10-15 23:09:16.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-10-15 23:09:16.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-10-15 23:09:16.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-10-15 23:09:16.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:16.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-10-15 23:09:16.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-10-15 23:09:16.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:16.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-15 23:09:17.020][biodb::testThat]
biodb.INFO [2023-10-15 23:09:17.023][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-10-15 23:09:17.025][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:17.027][biodb::testThat]
biodb.TRACE[2023-10-15 23:09:17.040][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:17.043][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:17.045][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:17.050][ef$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:09:17.053][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-10-15 23:09:17.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:17.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:17.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:17.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:17.154][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:17.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:17.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:17.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:17.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:17.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:17.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:17.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:09:17.191][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-10-15 23:09:17.205][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[2023-10-15 23:09:17.287][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:09:17.339][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-10-15 23:09:17.345][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:09:17.352][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-10-15 23:09:17.356][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-10-15 23:09:17.403][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:17.411][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:17.413][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:17.415][ef$get] fields variable is a list.
biodb.INFO [2023-10-15 23:09:17.431][biodb::testThat]
biodb.INFO [2023-10-15 23:09:17.433][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-10-15 23:09:17.442][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:17.445][biodb::testThat]
biodb.TRACE[2023-10-15 23:09:17.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:17.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:17.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:17.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:17.562][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:17.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:17.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:17.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:17.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:17.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:17.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:17.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:09:18.001][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[2023-10-15 23:09:18.009][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:09:18.015][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-10-15 23:09:18.018][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:09:18.021][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-10-15 23:09:18.082][biodb::testThat]
biodb.INFO [2023-10-15 23:09:18.084][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-10-15 23:09:18.086][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:18.087][biodb::testThat]
biodb.TRACE[2023-10-15 23:09:18.171][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 23:09:18.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 23:09:18.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:18.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:18.183][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 23:09:18.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 23:09:18.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:18.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:18.198][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-15 23:09:18.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-15 23:09:18.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:18.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:18.209][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-15 23:09:18.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-15 23:09:18.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:18.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:18.352][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 23:09:18.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 23:09:18.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:18.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:18.361][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 23:09:18.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 23:09:18.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:18.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:18.372][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-15 23:09:18.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-15 23:09:18.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:18.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:18.383][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-15 23:09:18.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-15 23:09:18.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:18.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-15 23:09:18.414][biodb::testThat]
biodb.INFO [2023-10-15 23:09:18.420][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-10-15 23:09:18.422][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:18.424][biodb::testThat]
biodb.INFO [2023-10-15 23:09:18.459][biodb::testThat]
biodb.INFO [2023-10-15 23:09:18.461][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-10-15 23:09:18.468][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:18.470][biodb::testThat]
biodb.INFO [2023-10-15 23:09:18.495][biodb::testThat]
biodb.INFO [2023-10-15 23:09:18.497][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-10-15 23:09:18.500][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:18.502][biodb::testThat]
biodb.DEBUG[2023-10-15 23:09:18.515][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-10-15 23:09:20.096][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-10-15 23:09:20.767][biodb::testThat]
biodb.INFO [2023-10-15 23:09:20.769][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-10-15 23:09:20.771][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:20.773][biodb::testThat]
biodb.TRACE[2023-10-15 23:09:20.789][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:20.791][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:20.793][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:20.795][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:20.797][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:20.800][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:20.802][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:20.804][ef$get] fields variable is a list.
biodb.INFO [2023-10-15 23:09:20.808][biodb::testThat]
biodb.INFO [2023-10-15 23:09:20.810][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2023-10-15 23:09:20.812][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:20.814][biodb::testThat]
biodb.TRACE[2023-10-15 23:09:20.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:20.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:20.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:20.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:20.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:20.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:20.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:20.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:20.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:20.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:20.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:20.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:09:21.093][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[2023-10-15 23:09:21.100][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:09:21.103][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-10-15 23:09:21.106][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:09:21.110][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-10-15 23:09:21.321][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[2023-10-15 23:09:21.330][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:09:21.333][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-10-15 23:09:21.338][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:09:21.341][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-10-15 23:09:21.392][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-15 23:09:21.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-15 23:09:21.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:21.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:21.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-15 23:09:21.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-15 23:09:21.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:21.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:21.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:21.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:21.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:21.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:21.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:21.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:21.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:21.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:21.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:21.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:21.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:21.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:21.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:21.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:21.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:21.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:21.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:21.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:21.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:21.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:09:21.538][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[2023-10-15 23:09:21.549][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:09:21.552][cch$loadFileContent] Trying to load 1 files from cache: [1]: "304383a7dc8c451be84009e31d831359".
biodb.TRACE[2023-10-15 23:09:21.555][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:09:21.645][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content".
biodb.DEBUG[2023-10-15 23:09:24.525][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[2023-10-15 23:09:24.536][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:09:24.543][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7f71825f1888a7b29e4b8407502d21e3".
biodb.TRACE[2023-10-15 23:09:24.546][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:09:24.550][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content".
biodb.DEBUG[2023-10-15 23:09:24.627][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[2023-10-15 23:09:24.638][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:09:24.641][cch$loadFileContent] Trying to load 1 files from cache: [1]: "fd41c675dd237f33cdaafcbb15058c54".
biodb.TRACE[2023-10-15 23:09:24.644][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:09:24.648][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content".
biodb.TRACE[2023-10-15 23:09:24.704][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-15 23:09:24.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-15 23:09:24.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:24.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-15 23:09:24.748][biodb::testThat]
biodb.INFO [2023-10-15 23:09:24.750][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-10-15 23:09:24.757][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:24.759][biodb::testThat]
biodb.TRACE[2023-10-15 23:09:24.769][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-15 23:09:24.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-15 23:09:24.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:24.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:24.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-15 23:09:24.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-15 23:09:24.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:24.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:24.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:24.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:24.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:24.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:24.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:24.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:24.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:24.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:24.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:24.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:24.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:24.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:24.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:24.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:24.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:24.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:09:24.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:24.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:24.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:24.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:24.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:24.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:24.907][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[2023-10-15 23:09:24.915][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[2023-10-15 23:09:24.926][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:09:24.930][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-10-15 23:09:24.933][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:09:24.999][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-10-15 23:09:27.403][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-10-15 23:09:27.555][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-10-15 23:09:27.558][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-10-15 23:09:27.561][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-10-15 23:09:27.573][loadFileContents] Loaded 2 files from 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[2023-10-15 23:09:27.577][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-15 23:09:27.580][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-10-15 23:09:27.582][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-15 23:09:27.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:27.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:27.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:27.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:27.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:27.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:27.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:09:27.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:27.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:27.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:27.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:27.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:09:27.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:09:27.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:09:27.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:09:27.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.707][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:09:27.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:09:27.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.726][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:09:27.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:09:27.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.747][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:27.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:27.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.768][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:27.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:27.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.783][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:27.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:27.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.800][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:27.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:27.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.821][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:09:27.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:27.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.833][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:09:27.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:27.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.856][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:27.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:27.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.876][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:27.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:27.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.938][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:27.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:27.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:27.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:27.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.963][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:09:27.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:27.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.976][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 23:09:27.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:27.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:27.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:27.999][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:28.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:28.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:28.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:28.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.031][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:09:28.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:28.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.046][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.056][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.081][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:09:28.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:28.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:28.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:28.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:28.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:28.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:28.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:09:28.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:09:28.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:09:28.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.213][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:09:28.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:09:28.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.225][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:09:28.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:09:28.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.238][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:28.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:28.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.249][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:28.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:09:28.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.263][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:28.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:28.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.275][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:28.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:09:28.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.287][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:09:28.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:28.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.300][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:09:28.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:28.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.314][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:28.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:28.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.326][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:09:28.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:09:28.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:28.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:28.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.352][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:28.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:28.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.362][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:09:28.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:28.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.404][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 23:09:28.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:28.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:28.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:28.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:09:28.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:28.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.438][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:09:28.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:09:28.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.452][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.462][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.486][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:28.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:28.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:09:28.595][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-10-15 23:09:28.622][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-15 23:09:28.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:28.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:28.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:28.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:28.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:28.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:28.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:09:28.656][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.671][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.682][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:28.684][private$selectFields]
biodb.TRACE[2023-10-15 23:09:28.686][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 23:09:28.692][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 23:09:28.694][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:28.696][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.699][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.702][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.704][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.706][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.709][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.711][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.718][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.720][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:28.723][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:28.725][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.727][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.729][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.732][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.734][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 23:09:28.737][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.750][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.760][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.836][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-10-15 23:09:28.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:28.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:28.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:28.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:28.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:28.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:28.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:09:28.875][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.888][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.900][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:28.902][private$selectFields]
biodb.TRACE[2023-10-15 23:09:28.909][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 23:09:28.911][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 23:09:28.913][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:28.915][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.921][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.923][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.925][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.929][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.933][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.936][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.938][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.943][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:28.946][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:28.949][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.952][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.959][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.961][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.963][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 23:09:28.965][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.977][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:28.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:28.993][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:28.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.007][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-10-15 23:09:29.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:29.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:29.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:29.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:29.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:29.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:29.041][FUN] Functions in observer BiodbConfig: [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[2023-10-15 23:09:29.044][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.055][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.067][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:29.072][private$selectFields]
biodb.TRACE[2023-10-15 23:09:29.074][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 23:09:29.081][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 23:09:29.083][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:29.086][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.090][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.094][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.096][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.099][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.101][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.103][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.110][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.113][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:29.115][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:29.117][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.126][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.128][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.130][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.132][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 23:09:29.134][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.146][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.157][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:29.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.170][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-10-15 23:09:29.172][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-10-15 23:09:29.177][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-15 23:09:29.207][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-15 23:09:29.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-15 23:09:29.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-15 23:09:29.238][biodb::testThat]
biodb.INFO [2023-10-15 23:09:29.274][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-10-15 23:09:29.280][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:29.283][biodb::testThat]
biodb.TRACE[2023-10-15 23:09:29.293][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-15 23:09:29.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-15 23:09:29.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-15 23:09:29.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-15 23:09:29.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:29.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:29.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:29.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:29.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:29.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:29.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:29.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:29.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:29.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:29.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:09:29.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:29.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:29.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:29.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:29.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:29.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:29.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:29.599][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[2023-10-15 23:09:29.609][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:09:29.612][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5652f5994fce967a05a065a71bac3ed6".
biodb.TRACE[2023-10-15 23:09:29.615][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:09:29.675][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content".
biodb.DEBUG[2023-10-15 23:09:32.396][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-15 23:09:32.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:32.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:32.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:32.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:32.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:32.500][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:32.502][FUN] Functions in observer BiodbConfig: [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[2023-10-15 23:09:32.540][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.551][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.631][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:32.635][private$selectFields]
biodb.TRACE[2023-10-15 23:09:32.637][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 23:09:32.640][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 23:09:32.649][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:32.651][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.653][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.655][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.659][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.661][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.664][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.666][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.670][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.706][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:32.742][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:32.745][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.747][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.749][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.753][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.756][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 23:09:32.758][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.771][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.781][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.794][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-10-15 23:09:32.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:32.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:32.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:32.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:32.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:32.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:32.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:09:32.827][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.836][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.847][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:32.853][private$selectFields]
biodb.TRACE[2023-10-15 23:09:32.855][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 23:09:32.857][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 23:09:32.859][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:32.861][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.867][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.869][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.870][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.872][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.879][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.881][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.883][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.885][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:32.887][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:32.892][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.895][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.897][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.899][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.901][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 23:09:32.905][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.918][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.929][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.939][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-10-15 23:09:32.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:32.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:32.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:32.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:32.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:32.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:32.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:09:32.974][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.986][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:32.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:32.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:32.997][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:32.999][private$selectFields]
biodb.TRACE[2023-10-15 23:09:33.003][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 23:09:33.005][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 23:09:33.007][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:33.009][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:33.011][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:33.016][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:33.018][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:33.020][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:33.023][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:33.025][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:33.028][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:33.030][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:33.032][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:33.034][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:33.037][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:33.039][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:33.041][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:33.043][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 23:09:33.045][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:33.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:33.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:33.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:33.055][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:33.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:33.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:33.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:33.067][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:33.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:33.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:33.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:33.106][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-10-15 23:09:33.109][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-10-15 23:09:33.112][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-15 23:09:33.141][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-15 23:09:33.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-15 23:09:33.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:33.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-15 23:09:33.171][biodb::testThat]
biodb.INFO [2023-10-15 23:09:33.173][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-10-15 23:09:33.175][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:33.177][biodb::testThat]
biodb.TRACE[2023-10-15 23:09:33.185][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-15 23:09:33.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-15 23:09:33.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:33.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:33.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-15 23:09:33.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-15 23:09:33.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:33.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:33.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:33.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:33.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:33.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:33.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:33.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:33.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:33.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:33.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:33.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:33.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:33.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:33.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:33.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:09:33.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:33.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:09:33.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:33.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:33.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:33.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:33.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:33.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:33.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:33.307][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[2023-10-15 23:09:33.317][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:09:33.320][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-10-15 23:09:33.324][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:09:33.380][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-10-15 23:09:36.045][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-15 23:09:36.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:36.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:36.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:36.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:36.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:36.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:36.082][FUN] Functions in observer BiodbConfig: [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[2023-10-15 23:09:36.084][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.100][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.115][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:36.117][private$selectFields]
biodb.TRACE[2023-10-15 23:09:36.119][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 23:09:36.121][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 23:09:36.128][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:36.131][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.133][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.135][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.141][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.144][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.146][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.148][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.155][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.157][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:36.159][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:36.161][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.164][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.168][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.170][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.173][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 23:09:36.175][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.193][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.205][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.220][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-10-15 23:09:36.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:36.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:36.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:36.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:36.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:36.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:36.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:09:36.259][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.270][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.281][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:36.284][private$selectFields]
biodb.TRACE[2023-10-15 23:09:36.286][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 23:09:36.287][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 23:09:36.293][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:36.295][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.298][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.300][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.302][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.308][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.310][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.313][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.315][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.320][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:36.322][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:36.324][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.327][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.335][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.337][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.339][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 23:09:36.341][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.360][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.371][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.388][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-10-15 23:09:36.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:36.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:36.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:36.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:36.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:36.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:36.427][FUN] Functions in observer BiodbConfig: [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[2023-10-15 23:09:36.430][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.448][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.458][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:36.460][private$selectFields]
biodb.TRACE[2023-10-15 23:09:36.462][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 23:09:36.464][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 23:09:36.475][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:36.477][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.479][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.481][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.483][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.488][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.490][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.493][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.495][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.504][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:36.507][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:09:36.510][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.517][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.519][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.522][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.525][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 23:09:36.530][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.547][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.566][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:36.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:36.583][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-10-15 23:09:36.585][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-10-15 23:09:36.588][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-15 23:09:36.686][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-15 23:09:36.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-15 23:09:36.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:36.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-15 23:09:36.717][biodb::testThat]
biodb.INFO [2023-10-15 23:09:36.719][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2023-10-15 23:09:36.722][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:36.728][biodb::testThat]
biodb.DEBUG[2023-10-15 23:09:36.734][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-10-15 23:09:36.737][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-15 23:09:36.749][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-10-15 23:09:36.753][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-15 23:09:36.761][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-15 23:09:36.764][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-15 23:09:36.767][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-15 23:09:36.769][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-15 23:09:36.776][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-15 23:09:36.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:36.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:36.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:36.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:36.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:36.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:36.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:36.853][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-10-15 23:09:36.877][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:36.881][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:36.884][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 23:09:37.533][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:37.536][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:37.538][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[2023-10-15 23:09:37.542][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 23:09:38.228][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 23:09:38.231][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:38.233][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:38.277][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 23:09:38.987][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:38.990][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:38.993][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[2023-10-15 23:09:38.995][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 23:09:39.864][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 23:09:39.866][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:39.868][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:39.871][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 23:09:40.591][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:40.593][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:40.596][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[2023-10-15 23:09:40.599][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 23:09:41.325][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 23:09:41.327][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:41.330][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:41.334][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 23:09:42.028][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:42.030][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:42.033][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[2023-10-15 23:09:42.036][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 23:09:42.917][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 23:09:42.919][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:42.922][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:42.925][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 23:09:43.661][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:43.664][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:43.667][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[2023-10-15 23:09:43.669][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 23:09:44.493][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 23:09:44.495][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:44.498][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:44.501][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 23:09:45.263][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:45.265][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:45.268][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[2023-10-15 23:09:45.271][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 23:09:46.213][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 23:09:46.216][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:46.218][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:46.222][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 23:09:46.941][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:46.943][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:46.946][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[2023-10-15 23:09:46.948][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 23:09:47.776][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 23:09:47.779][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:47.781][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:47.785][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 23:09:48.508][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:48.510][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:48.513][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[2023-10-15 23:09:48.515][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 23:09:49.207][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 23:09:49.209][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:49.212][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:49.215][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 23:09:49.978][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:49.980][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:49.982][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[2023-10-15 23:09:49.984][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 23:09:50.847][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 23:09:50.849][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:50.851][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:50.854][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 23:09:51.545][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:51.547][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:51.550][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[2023-10-15 23:09:51.552][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 23:09:52.171][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2023-10-15 23:09:52.177][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-10-15 23:09:52.180][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-15 23:09:52.183][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-10-15 23:09:52.186][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-15 23:09:52.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:52.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:52.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:52.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:52.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:52.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:52.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:09:52.215][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:52.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:52.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:52.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:52.224][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:52.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:09:52.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:52.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:52.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:52.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:52.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:52.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:52.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:52.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:52.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:52.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:52.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:52.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:52.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:52.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:52.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:52.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:52.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:52.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:52.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:52.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:52.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:52.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:09:52.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:09:52.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:09:52.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:09:52.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:09:52.285][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-10-15 23:09:52.287][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-10-15 23:09:52.308][biodb::testThat]
biodb.INFO [2023-10-15 23:09:52.310][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-10-15 23:09:52.312][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:09:52.315][biodb::testThat]
biodb.DEBUG[2023-10-15 23:09:52.331][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-10-15 23:09:52.334][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-10-15 23:09:52.336][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-10-15 23:09:52.339][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-10-15 23:09:52.342][cch$loadFileContent] file.exist = [2]: "FALSE, TRUE".
biodb.TRACE[2023-10-15 23:09:52.345][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv".
biodb.DEBUG[2023-10-15 23:09:52.348][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-15 23:09:52.350][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-15 23:09:52.352][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-15 23:09:52.354][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-15 23:09:52.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:09:52.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:09:52.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:09:52.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:09:52.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:09:52.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:09:52.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:09:52.479][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-10-15 23:09:52.539][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:52.541][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:52.551][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 23:09:53.334][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:53.336][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:53.339][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 23:09:53.341][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 23:09:54.091][private$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[2023-10-15 23:09:54.094][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:54.096][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:54.098][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 23:09:54.813][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:54.815][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:54.817][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 23:09:54.819][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 23:09:55.764][private$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[2023-10-15 23:09:55.766][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:55.768][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:55.771][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 23:09:56.485][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:56.487][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:56.489][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 23:09:56.491][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 23:09:57.245][private$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[2023-10-15 23:09:57.247][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:57.250][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:57.253][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 23:09:57.945][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:57.947][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:57.949][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 23:09:57.951][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 23:09:58.581][private$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[2023-10-15 23:09:58.583][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:09:58.586][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:09:58.589][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 23:09:59.312][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:09:59.351][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:09:59.353][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 23:09:59.355][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 23:10:00.141][private$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[2023-10-15 23:10:00.143][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:10:00.146][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:10:00.149][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 23:10:00.881][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:10:00.883][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:10:00.886][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 23:10:00.888][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 23:10:01.723][private$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[2023-10-15 23:10:01.725][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:10:01.727][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:10:01.730][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 23:10:02.437][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:10:02.439][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:10:02.442][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 23:10:02.444][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 23:10:03.185][private$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[2023-10-15 23:10:03.187][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:10:03.189][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:10:03.192][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 23:10:04.027][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:10:04.030][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:10:04.039][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 23:10:04.041][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 23:10:04.942][private$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[2023-10-15 23:10:04.944][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:10:04.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:10:04.949][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 23:10:05.703][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:10:05.705][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:10:05.707][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 23:10:05.710][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 23:10:06.596][private$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[2023-10-15 23:10:06.598][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:10:06.600][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:10:06.603][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 23:10:07.337][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 23:10:07.339][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 23:10:07.341][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 23:10:07.343][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 23:10:08.196][private$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.TRACE[2023-10-15 23:10:08.228][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv"
biodb.DEBUG[2023-10-15 23:10:08.285][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-15 23:10:08.288][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-10-15 23:10:08.290][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-15 23:10:08.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:10:08.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:08.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:08.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:08.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:08.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:08.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:10:08.319][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:08.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:08.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.328][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:08.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:08.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:08.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:08.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:10:08.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:10:08.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:08.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:08.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:08.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:08.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:08.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:10:08.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:08.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:08.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:08.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:08.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:08.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:08.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:08.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:08.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.464][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:10:08.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:10:08.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.475][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:10:08.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:10:08.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.489][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:10:08.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:10:08.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.501][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:10:08.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:10:08.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.510][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:08.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:08.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.537][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:08.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:08.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.546][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:08.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:08.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.554][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:08.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:08.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.562][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:10:08.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:08.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.571][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:10:08.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:08.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.585][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:08.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:08.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.597][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:08.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:08.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.609][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:08.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:08.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:08.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:08.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.635][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:10:08.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:08.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.656][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 23:10:08.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:08.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.664][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:08.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:08.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:08.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:08.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.683][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:10:08.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:08.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.693][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:08.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:08.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:08.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:08.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.828][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:08.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:08.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:08.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:08.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:08.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:08.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.868][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:08.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:08.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.882][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:08.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:08.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:08.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:08.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.899][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:08.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:08.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:08.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:08.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:08.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:08.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:08.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:08.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:08.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:08.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:08.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:08.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:08.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:08.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:08.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:08.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:08.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:08.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:09.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:09.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:09.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:09.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:09.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:09.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:09.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:09.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:09.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:09.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:09.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:09.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:09.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:09.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:09.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:09.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:09.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:10:09.062][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-10-15 23:10:09.064][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-10-15 23:10:09.066][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-10-15 23:10:09.115][biodb::testThat]
biodb.INFO [2023-10-15 23:10:09.118][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2023-10-15 23:10:09.120][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:10:09.123][biodb::testThat]
biodb.INFO [2023-10-15 23:10:09.194][biodb::testThat]
biodb.INFO [2023-10-15 23:10:09.196][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2023-10-15 23:10:09.197][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:10:09.202][biodb::testThat]
biodb.INFO [2023-10-15 23:10:09.234][biodb::testThat]
biodb.INFO [2023-10-15 23:10:09.236][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2023-10-15 23:10:09.239][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:10:09.242][biodb::testThat]
biodb.DEBUG[2023-10-15 23:10:09.253][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[2023-10-15 23:10:09.260][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:10:09.265][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-10-15 23:10:09.270][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:10:09.331][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.TRACE[2023-10-15 23:10:11.543][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:11.545][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:11.547][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:11.549][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:11.557][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:11.560][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:11.562][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:11.564][ef$get] fields variable is a list.
biodb.INFO [2023-10-15 23:10:11.568][biodb::testThat]
biodb.INFO [2023-10-15 23:10:11.572][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2023-10-15 23:10:11.574][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:10:11.576][biodb::testThat]
biodb.ERROR[2023-10-15 23:10:11.619][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-10-15 23:10:11.662][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-10-15 23:10:11.703][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-15 23:10:11.708][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-10-15 23:10:11.710][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-10-15 23:10:11.712][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-15 23:10:11.714][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:11.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:11.719][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:11.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:11.722][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:11.724][FUN] Functions in observer BiodbConfig: [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 [2023-10-15 23:10:11.752][biodb::testContext]
biodb.INFO [2023-10-15 23:10:11.779][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-15 23:10:11.781][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-10-15 23:10:11.783][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-15 23:10:11.785][biodb::testContext]
biodb.INFO [2023-10-15 23:10:11.791][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-15 23:10:11.797][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-15 23:10:11.812][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 23:10:11.816][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-15 23:10:11.818][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-15 23:10:11.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:11.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:11.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:11.829][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-15 23:10:11.832][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-15 23:10:11.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:11.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:11.844][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[2023-10-15 23:10:11.846][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-15 23:10:11.848][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-15 23:10:11.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:11.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:11.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:11.860][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-15 23:10:11.863][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-15 23:10:11.866][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-15 23:10:11.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:11.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:11.875][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[2023-10-15 23:10:11.877][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-15 23:10:11.880][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-15 23:10:11.901][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-15 23:10:11.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:11.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:11.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:11.910][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-15 23:10:11.912][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-15 23:10:11.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:11.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:11.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:11.921][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-15 23:10:11.926][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-15 23:10:11.928][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-15 23:10:11.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:11.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:11.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:11.944][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-15 23:10:11.947][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-15 23:10:11.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:11.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:11.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:11.959][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-15 23:10:11.961][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-15 23:10:11.963][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-15 23:10:11.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:11.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:11.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:11.976][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-15 23:10:11.978][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-15 23:10:11.983][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-15 23:10:11.986][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-15 23:10:11.988][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-15 23:10:11.994][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-15 23:10:11.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.006][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-15 23:10:12.011][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-15 23:10:12.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.021][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-15 23:10:12.023][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-15 23:10:12.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.037][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-15 23:10:12.039][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-15 23:10:12.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.050][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-15 23:10:12.052][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-15 23:10:12.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.068][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-15 23:10:12.070][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-15 23:10:12.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.085][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-15 23:10:12.087][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-15 23:10:12.115][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-15 23:10:12.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.134][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-15 23:10:12.136][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-15 23:10:12.139][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-15 23:10:12.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.148][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-15 23:10:12.153][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:12.156][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-15 23:10:12.159][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.161][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:10:12.164][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.169][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:10:12.171][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:12.173][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:10:12.176][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 23:10:12.183][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:10:12.186][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.193][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-15 23:10:12.196][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:10:12.199][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.201][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.206][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 23:10:12.206][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 23:10:12.206][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-15 23:10:12.206][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-15 23:10:12.206][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-15 23:10:12.209][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:10:12.212][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:12.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:12.218][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:10:12.222][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:12.225][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:12.227][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:10:12.232][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.236][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:10:12.238][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:10:12.245][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:12.248][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.256][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-15 23:10:12.261][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:12.264][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-15 23:10:12.267][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.270][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:10:12.272][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.274][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:10:12.277][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:12.279][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:10:12.282][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-15 23:10:12.284][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:10:12.287][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.295][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-15 23:10:12.297][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:10:12.299][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.302][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.311][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 23:10:12.311][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 23:10:12.311][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-15 23:10:12.311][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-15 23:10:12.311][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-15 23:10:12.313][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:10:12.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:12.318][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:12.325][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:10:12.328][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:12.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:12.332][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:10:12.337][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.339][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:10:12.342][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:10:12.344][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:12.347][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.370][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-15 23:10:12.379][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.382][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-15 23:10:12.385][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.389][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:10:12.391][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.394][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:10:12.396][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:12.400][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:10:12.403][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 23:10:12.406][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:10:12.412][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:12.415][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-15 23:10:12.418][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:10:12.421][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.432][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.434][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.437][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:10:12.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:12.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:12.451][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:10:12.453][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:12.462][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:12.471][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:10:12.473][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.477][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:10:12.482][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:10:12.484][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:12.487][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.490][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-15 23:10:12.495][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.505][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-15 23:10:12.508][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.510][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:10:12.516][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.519][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:10:12.521][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:12.524][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:10:12.527][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-15 23:10:12.529][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:10:12.534][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:12.537][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-15 23:10:12.540][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:10:12.542][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.548][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:12.550][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.573][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:10:12.584][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:12.588][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:12.591][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:10:12.593][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:12.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:12.602][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:10:12.605][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.609][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:10:12.611][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:10:12.621][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:12.624][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:12.629][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 23:10:12.631][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.837][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[2023-10-15 23:10:12.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:12.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.924][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[2023-10-15 23:10:12.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:12.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:12.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:12.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:12.942][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[2023-10-15 23:10:12.945][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-15 23:10:12.954][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-15 23:10:12.958][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-15 23:10:12.969][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-15 23:10:12.972][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-15 23:10:12.975][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-15 23:10:12.981][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-15 23:10:12.984][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-15 23:10:12.987][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-15 23:10:12.993][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-15 23:10:12.996][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-15 23:10:13.000][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-15 23:10:13.007][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-15 23:10:13.010][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-15 23:10:13.013][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-15 23:10:13.017][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-15 23:10:13.020][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-15 23:10:13.024][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-15 23:10:13.027][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-15 23:10:13.030][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-15 23:10:13.034][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-15 23:10:13.042][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-15 23:10:13.046][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-15 23:10:13.069][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-15 23:10:13.075][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-15 23:10:13.079][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-15 23:10:13.084][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-15 23:10:13.088][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-15 23:10:13.094][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-15 23:10:13.098][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-15 23:10:13.102][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-15 23:10:13.106][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-15 23:10:13.109][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-15 23:10:13.114][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-15 23:10:13.118][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-15 23:10:13.123][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-15 23:10:13.128][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-15 23:10:13.134][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-15 23:10:13.137][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-15 23:10:13.140][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-15 23:10:13.146][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-15 23:10:13.150][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-15 23:10:13.153][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-15 23:10:13.158][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-15 23:10:13.162][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-15 23:10:13.165][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-15 23:10:13.169][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-15 23:10:13.175][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-15 23:10:13.178][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-15 23:10:13.182][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-15 23:10:13.186][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-15 23:10:13.190][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-15 23:10:13.201][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-15 23:10:13.205][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-15 23:10:13.208][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-15 23:10:13.213][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-15 23:10:13.219][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-15 23:10:13.222][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-15 23:10:13.226][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-15 23:10:13.233][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-15 23:10:13.236][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-15 23:10:13.239][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-15 23:10:13.245][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-15 23:10:13.248][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-15 23:10:13.253][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-15 23:10:13.257][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-15 23:10:13.261][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-15 23:10:13.264][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-15 23:10:13.267][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-15 23:10:13.271][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-15 23:10:13.275][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-15 23:10:13.280][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-15 23:10:13.284][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-15 23:10:13.287][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-15 23:10:13.291][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-15 23:10:13.295][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-15 23:10:13.301][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-15 23:10:13.304][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-15 23:10:13.307][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-15 23:10:13.315][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-15 23:10:13.319][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-15 23:10:13.322][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-15 23:10:13.330][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-15 23:10:13.348][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-15 23:10:13.352][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-15 23:10:13.355][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 23:10:13.358][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.362][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.570][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[2023-10-15 23:10:13.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.606][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[2023-10-15 23:10:13.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:13.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:13.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:13.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:13.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:13.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:13.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:13.719][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-10-15 23:10:13.722][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 23:10:13.731][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:13.756][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-10-15 23:10:13.759][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:13.768][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:10:13.770][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:13.773][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:10:13.775][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:13.780][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:10:13.783][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 23:10:13.785][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:10:13.788][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:13.794][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-10-15 23:10:13.796][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:10:13.799][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-10-15 23:10:13.799][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-10-15 23:10:13.799][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-10-15 23:10:13.799][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-10-15 23:10:13.799][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-10-15 23:10:13.799][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-10-15 23:10:13.799][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-10-15 23:10:13.799][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-10-15 23:10:13.799][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-10-15 23:10:13.801][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:13.807][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 23:10:13.807][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 23:10:13.811][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:10:13.813][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:13.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:13.817][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:10:13.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:13.826][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:13.828][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:10:13.830][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-15 23:10:13.830][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-10-15 23:10:13.853][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:10:13.855][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:10:13.857][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:13.859][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:13.862][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-10-15 23:10:13.866][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-15 23:10:13.875][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 23:10:13.877][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-10-15 23:10:13.880][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 23:10:13.884][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-10-15 23:10:13.891][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-15 23:10:13.893][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-15 23:10:13.896][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-10-15 23:10:13.899][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-10-15 23:10:13.907][biodb::testThat]
biodb.INFO [2023-10-15 23:10:13.910][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-10-15 23:10:13.912][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:10:13.916][biodb::testThat]
biodb.DEBUG[2023-10-15 23:10:13.925][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[2023-10-15 23:10:13.938][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:10:13.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:10:13.951][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-10-15 23:10:14.701][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2023-10-15 23:10:15.508][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 23:10:15.512][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-10-15 23:10:15.535][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-10-15 23:10:15.624][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2023-10-15 23:10:15.631][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:10:15.634][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4ae22a112f570b93d2a956448ab71bd0".
biodb.TRACE[2023-10-15 23:10:15.637][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:10:15.640][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content".
biodb.INFO [2023-10-15 23:10:15.664][biodb::testThat]
biodb.INFO [2023-10-15 23:10:15.666][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-10-15 23:10:15.668][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:10:15.670][biodb::testThat]
biodb.INFO [2023-10-15 23:10:15.732][biodb::testThat]
biodb.INFO [2023-10-15 23:10:15.738][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-10-15 23:10:15.740][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:10:15.743][biodb::testThat]
biodb.DEBUG[2023-10-15 23:10:15.750][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-10-15 23:10:15.769][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:10:15.772][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:10:15.811][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-10-15 23:10:16.551][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-10-15 23:10:17.128][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 23:10:17.133][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-10-15 23:10:17.141][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-10-15 23:10:17.152][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[2023-10-15 23:10:17.159][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:10:17.162][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-10-15 23:10:17.164][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:10:17.167][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-10-15 23:10:17.199][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[2023-10-15 23:10:17.206][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:10:17.209][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:10:17.213][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-10-15 23:10:17.959][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2023-10-15 23:10:18.581][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 23:10:18.589][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-10-15 23:10:18.650][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-10-15 23:10:18.672][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2023-10-15 23:10:18.681][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 23:10:18.690][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 23:10:18.694][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-10-15 23:10:20.211][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-10-15 23:10:21.875][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 23:10:21.878][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-10-15 23:10:21.918][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-10-15 23:10:22.209][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[2023-10-15 23:10:22.228][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:10:22.231][cch$loadFileContent] Trying to load 1 files from cache: [1]: "6821b039f49696a2484834eb67daa971".
biodb.TRACE[2023-10-15 23:10:22.234][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:10:22.246][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content".
biodb.INFO [2023-10-15 23:10:22.558][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-15 23:10:22.560][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-10-15 23:10:22.568][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-10-15 23:10:22.570][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-15 23:10:22.572][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:22.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:22.602][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:22.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:22.608][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.610][FUN] Functions in observer BiodbConfig: [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 [2023-10-15 23:10:22.619][biodb::testContext]
biodb.INFO [2023-10-15 23:10:22.621][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-15 23:10:22.623][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-10-15 23:10:22.625][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-15 23:10:22.628][biodb::testContext]
biodb.INFO [2023-10-15 23:10:22.633][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-15 23:10:22.637][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-15 23:10:22.650][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 23:10:22.668][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-15 23:10:22.671][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-15 23:10:22.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.676][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-15 23:10:22.678][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-15 23:10:22.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.685][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-15 23:10:22.687][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-15 23:10:22.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.695][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-15 23:10:22.697][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-15 23:10:22.699][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-15 23:10:22.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.707][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-15 23:10:22.709][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-15 23:10:22.760][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-15 23:10:22.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.772][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-15 23:10:22.774][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-15 23:10:22.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.788][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-15 23:10:22.790][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-15 23:10:22.792][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-15 23:10:22.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.806][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-15 23:10:22.811][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-15 23:10:22.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.819][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-15 23:10:22.823][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-15 23:10:22.825][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-15 23:10:22.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.835][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-15 23:10:22.837][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-15 23:10:22.839][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-15 23:10:22.842][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-15 23:10:22.845][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-15 23:10:22.848][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-15 23:10:22.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.858][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-15 23:10:22.861][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-15 23:10:22.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.869][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-15 23:10:22.871][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-15 23:10:22.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.880][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-15 23:10:22.882][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-15 23:10:22.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.911][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-15 23:10:22.913][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-15 23:10:22.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.919][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[2023-10-15 23:10:22.921][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-15 23:10:22.923][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-15 23:10:22.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.931][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-15 23:10:22.933][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-15 23:10:22.951][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-15 23:10:22.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.959][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-15 23:10:22.961][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-15 23:10:22.963][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-15 23:10:22.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:22.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:22.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:22.971][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-15 23:10:22.975][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:22.977][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-15 23:10:22.979][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:22.981][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:10:22.983][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:22.985][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:10:22.987][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:22.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:10:22.991][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 23:10:22.993][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:10:22.995][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.002][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-15 23:10:23.004][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:10:23.006][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.008][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.015][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 23:10:23.015][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 23:10:23.015][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-15 23:10:23.015][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-15 23:10:23.015][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-15 23:10:23.018][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:10:23.020][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:23.022][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:23.032][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:10:23.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:23.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:23.041][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:10:23.044][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.046][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:10:23.047][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:10:23.049][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:23.051][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.054][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-15 23:10:23.059][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:23.062][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-15 23:10:23.064][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.067][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:10:23.069][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.071][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:10:23.073][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:23.076][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:10:23.079][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-15 23:10:23.082][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:10:23.084][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.088][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-15 23:10:23.090][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:10:23.093][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.095][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.098][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 23:10:23.098][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 23:10:23.098][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-15 23:10:23.098][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-15 23:10:23.098][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-15 23:10:23.100][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:10:23.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:23.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:23.107][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:10:23.110][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:23.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:23.114][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:10:23.116][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.119][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:10:23.123][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:10:23.125][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:23.127][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.129][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-15 23:10:23.134][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.155][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-15 23:10:23.158][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.160][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:10:23.162][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.164][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:10:23.166][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:23.168][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:10:23.170][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 23:10:23.172][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:10:23.175][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:23.177][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-15 23:10:23.179][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:10:23.181][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.183][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.184][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.186][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:10:23.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:23.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:23.192][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:10:23.194][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:23.195][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:23.197][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:10:23.199][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.201][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:10:23.203][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:10:23.204][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:23.206][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.209][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-15 23:10:23.213][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.215][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-15 23:10:23.217][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.219][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:10:23.221][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.223][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:10:23.226][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:23.229][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:10:23.231][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-15 23:10:23.233][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:10:23.235][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:23.239][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-15 23:10:23.241][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:10:23.243][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.245][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:23.248][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.250][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:10:23.253][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:23.255][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:23.257][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:10:23.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:23.261][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:23.263][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:10:23.269][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.272][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:10:23.274][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:10:23.276][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:23.287][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:23.290][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 23:10:23.295][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.475][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[2023-10-15 23:10:23.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.491][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-15 23:10:23.495][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-15 23:10:23.499][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-15 23:10:23.506][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-15 23:10:23.509][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-15 23:10:23.513][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-15 23:10:23.520][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-15 23:10:23.523][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-15 23:10:23.526][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-15 23:10:23.532][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-15 23:10:23.536][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-15 23:10:23.539][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-15 23:10:23.543][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-15 23:10:23.547][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-15 23:10:23.550][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-15 23:10:23.556][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-15 23:10:23.559][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-15 23:10:23.562][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-15 23:10:23.567][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-15 23:10:23.570][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-15 23:10:23.573][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-15 23:10:23.577][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-15 23:10:23.581][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-15 23:10:23.584][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-15 23:10:23.589][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-15 23:10:23.592][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-15 23:10:23.595][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-15 23:10:23.600][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-15 23:10:23.603][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-15 23:10:23.606][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-15 23:10:23.631][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-15 23:10:23.636][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-15 23:10:23.640][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-15 23:10:23.643][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-15 23:10:23.668][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-15 23:10:23.671][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-15 23:10:23.673][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-15 23:10:23.676][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-15 23:10:23.679][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-15 23:10:23.682][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-15 23:10:23.684][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-15 23:10:23.687][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-15 23:10:23.691][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-15 23:10:23.694][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-15 23:10:23.697][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-15 23:10:23.701][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-15 23:10:23.705][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-15 23:10:23.708][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-15 23:10:23.712][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-15 23:10:23.716][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-15 23:10:23.719][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-15 23:10:23.722][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-15 23:10:23.726][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-15 23:10:23.729][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-15 23:10:23.732][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-15 23:10:23.735][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-15 23:10:23.739][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-15 23:10:23.742][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-15 23:10:23.745][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-15 23:10:23.748][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-15 23:10:23.750][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-15 23:10:23.754][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-15 23:10:23.757][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-15 23:10:23.760][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-15 23:10:23.763][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-15 23:10:23.766][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-15 23:10:23.770][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-15 23:10:23.777][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-15 23:10:23.784][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-15 23:10:23.787][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-15 23:10:23.790][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-15 23:10:23.798][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-15 23:10:23.801][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-15 23:10:23.804][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-15 23:10:23.833][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-15 23:10:23.836][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-15 23:10:23.839][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-15 23:10:23.843][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-15 23:10:23.846][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-15 23:10:23.849][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-15 23:10:23.852][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-15 23:10:23.855][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-15 23:10:23.859][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-15 23:10:23.862][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-15 23:10:23.865][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-15 23:10:23.867][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 23:10:23.869][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.891][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:23.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:23.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:23.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:23.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:23.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:23.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.941][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[2023-10-15 23:10:23.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:23.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:23.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:23.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:23.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:23.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:23.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:23.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:23.981][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[2023-10-15 23:10:23.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:23.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:23.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:23.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:23.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:23.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:24.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:24.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:24.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:24.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:24.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:24.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:24.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:24.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:24.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:24.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:24.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:24.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:24.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:24.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:24.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:24.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:24.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:24.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:24.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:24.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:24.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:24.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:24.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:24.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:24.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:24.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:24.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:24.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:24.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:24.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:24.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:24.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:24.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:24.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:24.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:24.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:24.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:24.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:24.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:24.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:24.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:24.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:24.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:24.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:24.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:24.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:24.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:24.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:24.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:24.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:24.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:24.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:24.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:24.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:24.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:24.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:24.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:24.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:24.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:24.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:24.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:24.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:24.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:24.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:24.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 23:10:24.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:24.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:24.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:24.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:24.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:24.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 23:10:24.186][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-10-15 23:10:24.190][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 23:10:24.195][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:24.200][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-10-15 23:10:24.203][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:24.206][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 23:10:24.210][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:24.213][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 23:10:24.215][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:24.218][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 23:10:24.221][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 23:10:24.224][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 23:10:24.226][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:24.229][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-10-15 23:10:24.233][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 23:10:24.235][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-10-15 23:10:24.235][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-10-15 23:10:24.235][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-10-15 23:10:24.235][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-10-15 23:10:24.235][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-10-15 23:10:24.235][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-10-15 23:10:24.235][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-10-15 23:10:24.235][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-10-15 23:10:24.235][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-10-15 23:10:24.238][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-15 23:10:24.241][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 23:10:24.241][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 23:10:24.244][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 23:10:24.246][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:24.248][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:24.251][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 23:10:24.253][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 23:10:24.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 23:10:24.263][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 23:10:24.271][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-15 23:10:24.271][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-10-15 23:10:24.273][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 23:10:24.275][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 23:10:24.277][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-15 23:10:24.282][self$setPropertyValue]
biodb.DEBUG[2023-10-15 23:10:24.285][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-10-15 23:10:24.288][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-15 23:10:24.296][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 23:10:24.298][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-10-15 23:10:24.301][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 23:10:24.304][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-10-15 23:10:24.306][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-15 23:10:24.308][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-15 23:10:24.311][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-10-15 23:10:24.313][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-10-15 23:10:24.317][biodb::testThat]
biodb.INFO [2023-10-15 23:10:24.319][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2023-10-15 23:10:24.321][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 23:10:24.323][biodb::testThat]
biodb.DEBUG[2023-10-15 23:10:24.331][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[2023-10-15 23:10:24.339][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 23:10:24.343][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-10-15 23:10:24.346][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 23:10:24.397][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-10-15 23:10:26.486][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-10-15 23:10:26.488][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-10-15 23:10:26.491][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-10-15 23:10:26.500][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-10-15 23:10:26.503][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[2023-10-15 23:10:26.506][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-15 23:10:26.513][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-10-15 23:10:26.517][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-15 23:10:26.520][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:10:26.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:26.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:26.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:26.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:26.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:26.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:10:26.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:26.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:26.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:26.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:26.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:26.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:26.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:26.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:26.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.632][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:10:26.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:10:26.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.640][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:10:26.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:10:26.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.649][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:26.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:26.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.661][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:26.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:26.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.670][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:26.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:26.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.679][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:26.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:26.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.688][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:10:26.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:26.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.697][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:10:26.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:26.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.707][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:26.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:26.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.721][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:26.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:26.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.738][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:26.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:26.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.749][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:26.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:26.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.760][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:10:26.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:26.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.772][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 23:10:26.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:26.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.784][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:26.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:26.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:26.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:26.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.806][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:10:26.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:26.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:26.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:26.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.834][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:26.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:26.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.976][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:26.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:26.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:26.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:26.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:26.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:26.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:27.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:27.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.023][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.037][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.072][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:10:27.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:10:27.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:27.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:27.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:27.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:27.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:27.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:10:27.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:27.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:27.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:27.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:27.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.212][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:10:27.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 23:10:27.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.224][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:10:27.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 23:10:27.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.234][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:27.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:27.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.244][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:27.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:27.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.255][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:27.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:27.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.267][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:27.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:27.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.281][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:10:27.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:27.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.292][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 23:10:27.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:27.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.321][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:27.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:27.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.331][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:27.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:27.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:27.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:27.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:27.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:27.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.359][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:10:27.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:27.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.372][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 23:10:27.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:27.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.417][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:27.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:27.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.452][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:27.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:27.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.490][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 23:10:27.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:27.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.500][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.511][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.575][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 23:10:27.694][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-10-15 23:10:27.702][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-15 23:10:27.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:10:27.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:27.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:27.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:27.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:27.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:27.731][FUN] Functions in observer BiodbConfig: [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[2023-10-15 23:10:27.736][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 23:10:27.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 23:10:27.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.748][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 23:10:27.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 23:10:27.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.762][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-15 23:10:27.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-15 23:10:27.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.772][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-15 23:10:27.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-15 23:10:27.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.786][private$selectFields] Fields none
biodb.TRACE[2023-10-15 23:10:27.789][private$selectFields]
biodb.TRACE[2023-10-15 23:10:27.791][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-10-15 23:10:27.796][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 23:10:27.798][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:10:27.800][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.803][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.805][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.807][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.809][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:27.811][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:27.813][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.815][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.818][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:27.820][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:27.822][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.824][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.827][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:27.831][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:27.833][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.835][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.837][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:27.842][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:27.844][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.846][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.849][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:27.874][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:27.876][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.879][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.881][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:27.884][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:27.887][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.889][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.891][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.895][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.897][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.899][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.902][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:27.904][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:27.907][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.910][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.913][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:27.915][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:27.918][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.920][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.922][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:27.924][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:27.926][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.929][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.931][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:27.935][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:27.938][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.944][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.946][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:27.949][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:27.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.953][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.959][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:27.961][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:27.963][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.966][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.971][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:27.973][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:27.976][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.978][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:27.984][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.987][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:27.989][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:27.998][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.001][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:10:28.003][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:10:28.011][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:28.014][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:28.016][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.017][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.023][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.026][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.028][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.030][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.032][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.035][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.038][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.040][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.042][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.048][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.053][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.055][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.058][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.060][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.063][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.066][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:28.068][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:28.071][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.073][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.076][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:28.079][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:28.086][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.089][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.092][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.094][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.098][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.100][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.102][private$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[2023-10-15 23:10:28.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:28.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:28.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:28.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:28.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:28.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:28.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.193][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.202][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.210][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.223][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.234][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.245][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.296][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:28.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:28.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.306][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:28.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:28.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.316][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:28.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:28.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.327][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:28.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:28.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:28.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:28.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.348][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:28.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:28.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.359][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.390][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.400][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.421][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2023-10-15 23:10:28.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 23:10:28.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:28.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:28.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:28.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:28.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:28.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 23:10:28.482][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 23:10:28.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 23:10:28.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.492][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 23:10:28.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 23:10:28.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.502][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-15 23:10:28.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-15 23:10:28.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.515][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-15 23:10:28.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-15 23:10:28.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.528][private$selectFields] Fields none
biodb.TRACE[2023-10-15 23:10:28.533][private$selectFields]
biodb.TRACE[2023-10-15 23:10:28.535][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-10-15 23:10:28.537][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 23:10:28.539][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:10:28.563][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:28.566][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:28.568][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.570][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.572][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.575][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.577][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.579][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.581][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.584][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.586][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.590][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.592][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.595][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.597][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.599][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.608][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.611][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.632][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.634][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.636][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:28.638][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:28.641][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.643][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.645][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:28.647][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:28.650][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.652][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.654][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.656][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.658][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.660][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.663][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:28.665][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:28.667][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.669][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.672][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.675][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.677][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.679][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.681][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.683][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.685][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.687][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.690][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.692][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.695][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.697][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.700][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.702][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.705][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.707][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.710][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:28.713][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:28.715][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.717][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.720][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:28.723][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:28.725][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.728][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.730][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.733][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.735][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.737][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.744][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:10:28.746][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-15 23:10:28.772][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:28.775][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:28.780][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.784][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.786][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.788][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.791][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.795][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.798][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.800][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.802][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.805][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.807][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.809][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.812][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.814][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.816][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.819][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:28.821][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.827][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.831][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:28.839][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:28.842][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.845][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.847][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:28.850][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:28.852][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.854][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.859][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.861][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:28.863][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.865][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.870][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-10-15 23:10:28.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:28.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:28.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:28.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:28.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 23:10:28.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 23:10:28.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 23:10:28.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.954][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.966][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.976][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 23:10:28.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.986][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:28.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:28.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:28.999][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:29.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:29.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.014][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:29.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 23:10:29.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:29.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:29.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:29.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:29.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:29.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 23:10:29.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.062][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:29.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:29.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.071][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:29.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:29.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.082][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 23:10:29.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 23:10:29.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.091][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:29.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:29.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:29.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:29.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 23:10:29.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 23:10:29.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.146][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:29.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:29.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.160][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:29.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:29.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.177][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:29.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 23:10:29.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 23:10:29.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 23:10:29.214][private$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[2023-10-15 23:10:29.216][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-10-15 23:10:29.219][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-10-15 23:10:29.239][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-15 23:10:29.246][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-10-15 23:10:29.249][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-10-15 23:10:29.255][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-15 23:10:29.257][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 23:10:29.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 23:10:29.267][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 23:10:29.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 23:10:29.272][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 23:10:29.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 165 ]
> 
> proc.time()
   user  system elapsed 
 32.271   1.951  83.027

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn4.0851.1237.351
LipidmapsStructureEntry0.8070.0211.151